Before I start, I never played Hunters Hunted II, so I'm taking everything from the pre edit production text, which "content-wise, [is] 99% complete" (direct quote). I found the concept interesting yet murky, so I'll follow the whole thing. Pardon me if I digress, I'm thinking this up as I read the book and write.
What are Plan Dice?
From the description in the book (Section "Investigation and Interpretation), the "plan" is meant to be an opportunity for the players to really get in-character and role-play the creation of a plan to find and defeat the vampires. The creators make the very good point that, given the effort the vampires put into being invisible, it's unlikely that the hunters—normal humans—know much (or anything at all) about them. More likely they witnessed the existence of one and decided they must do something about it.
Therefore, they must combine the information they have, try to anticipate the vampires' powers and ways to circumvent them, in order to complete their mission. They also have to deal with the fact that their plans might fail, which incentivises trying to foresee complications that they are unaware of. While planning is not mandatory, it gives an edge (or rather, removes the edge that vampires have from being invisible). The way to work this into the mechanics are plan dice.
How to earn them?
Planning is broken down in smaller tasks before the mission starts.
- Gathering information such as schedules and habits, which earns one die per piece of information actually used.
- Planning execution step by step: what is the objective of the mission? How to approach it? What are the tools needed? This earns one die per step in the plan.
- Assigning tasks to each character earns one die per task assigned to each character.
- Finding holes in the plan and changing it accordingly earns one die per change or per decision made by a character about the plan.
- Gearing up and training earns one die per character that spent at least half a day training with a tool.
- Personal preparations, such as living a will or spending time with family, earns one die per player that describes a scene of their characters preparation. A second die may be earned if the scene seems particularly appropriate to the characters nature. Alternatively, the character's Whirlpool pool can be refilled.
- Embracing chaos: In section "Things you don't plan for", the following mechanic is described:
During the planning phase, the players can take up to five extra Plan Dice to the usable total (that is, after the first total has been divided by the number of players). The Storyteller then rolls those dice (difficulty 8) before handing them over to the players. At some point during the mission, something random — not put in motion by the target or the characters — happens to the hunters. Whether it helps them or hurts them depends on how many successes the Storyteller rolls on these dice. For maximum effect, the Storyteller should keep the results of this roll secret, so that when the event occurs the players don’t immediately know if it will help or harm them
All dice are added to a single stack, which is then divided by the number of players in the party. So if you have, say, 20 Plan Dice and 4 players, the Plan Dice pool has 5 dice, which could be incremented to 10 through the above step. The book says nothing about divisions with remainder, which presumably means the remainder gets discarded.
How can I use them?
This last part is the actual answer to the OPs original question.
Plan Dice can be used during the execution of the plan to help compensate for unknown factors or unexpected turns of events.
That means that, should something happen that wasn't foreseen by the plan ("unexpected turns of events"), plan dice can be spent to make up for it. The following quotes will support this view.
This makes sense–if you put effort in thinking all that could happen, a lot of what actually happens is already accounted for and doesn't require much thinking before acting. If they don't have to waste time or energy with trivial tasks, they have more of it to spend on surprises.
The section "Changes to the Plan" describes possible uses of Plan Dice. I won't copy large chunks of it, just look at it for more details. Instead, I'll summarise my understanding of them and make a list.
- If the predicted number of enemies is larger than expected, Plan Dice can be used to change an existing part of the plan to use it against a different enemy instead of the intended one. They can **double* the ammount of dice used this way:
The characters were planning on luring the vampire out into the garden and then dropping a bunch of rocks taken from said garden from the nearby roof (...). Instead, the characters decide to use this strategy on the abnormally large mastiff with blood on its lips. If they put three Plan Dice into this action, they actually get six dice, but then they can’t use this part of the plan on the vampire himself.
- If the target is better armed than the characters (or, I assume, unexpectedly armed) and the characters have reasonable protective gear, they can add plan dice to soak up damage:
The characters break in and discover that not only is the bloodsucker awake, he’s packing a submachine gun. (...) if they have equipment that can reasonably counter their target’s use of weaponry (body armor, for instance), then the players can bolster that equipment’s effectiveness with Plan Dice. If using body armor to add to soak, for instance, the player can add Plan Dice to the soak roll.
- If the target has unforeseen powers, Plan Dice can be used to make the hunters less vulnerable. This doesn't apply to physical abilities, and can only be done if at least one die came from related intel in the plan:
If the hunters run afoul of a monster who displays a power or supernatural trait that their research does not represent, the players can add Plan Dice to any applicable resistance rolls or use them to increase the difficulty of powers used on them. (...) Two restrictions on this use of Plan Dice: First, the characters cannot use Plan Dice in this way unless they included some supernatural intel in their plan (that is, some of the Plan Dice had to come from planning to counteract a supernatural influence). Second, players cannot raise the difficulties of direct, physical attacks by using Plan Dice.
- If a hunter has an assigned task and doesn't do it, Plan Dice can be used to try to ensure that it gets done or isn't necessary.
In game terms, if one character does not undertake his appointed task, the other characters can apply Plan Dice to any attempt to make sure that part of the plan still happens or can be circumvented. This rule only applies if the action that the character did not perform was a specifically assigned action (that is, the players received Plan Dice for assigning it).
- In the event of a botched roll (not any simple failure), Plan Dice can be used in all subsequent rolls that are meant to clean up the mess. However this only applies if the character made any personal preparations
If the player added Plan Dice to the pool through putting the character’s affairs in order, the player can use Plan Dice to add to any roll meant to mitigate or correct the damage done by the botch. Note that this only applies in the event of a botch (see p. 250 of V20), not just a failure.
These are all the mentions of Plan Dice in the link, so I assume this is all.
 This one, to me, sounds like poor planning by the game creators—this encourages not predicting any powers but the least necessary. As a ST, I'd force the plan to account for any seen or mentioned powers-for instance, if any character witnessed shapeshifting, read Dracula or heard any vampire stories, shapeshifting has to be in the plan. Another alternative is to invert it to account for foreseen powers instead and see if it affects the gameplay too much. First solution would make the game harder as the hunters become more experienced, the latter would make it harder in the beginning and easier in the end (which could improve the odds against extremely powerful vampires)
 For this one, it's unclear if it refers to the character who botched the roll must be the one trying to fix it. I assume yes.
How to divide the dice?
As far as I've read it, which is admittedly little, the book doesn't specify this. I think it's something that you can decide among the players before it happens. Of course the ST can call Rule 0 and decide it alone.
One thing that might work is trying to divide the pool equally among the players and each can decide what to do with theirs, including giving to someone else. The fate of the remainder can be decided democratically.