The most important thing to understand here is that the Missle Pool is NEVER in contest with the Combat Pool. It works completely differently.
Melee fighters or... targets, don't have a lot of options to deal with missle weapons. I'll break down the general rules then go to your examples.
Get behind cover
If you are behind something they can't shoot through, you are safe. That's ideal. If you drop prone, you drastically limit what targets they can go for. If nothing else, you can declare to hold your shield up and cover a give section of your body (based on how big the shield is). Notice that if you're doing that, you can't really use your shield to help in melee.
This is pretty easy to do as long as you know there's someone targeting you. Or, if you're in the middle of a melee. This ups the attacker's MP cost, which is less dice they can use to shoot at you.
Range increases the ATN difficulty, so moving away erratically is going to give you a lot of benefit.
Notice that all three of the above are primarily positional - you're best off trying them in the rounds the shooter is aiming at you, and you are not going to get as much benefit in the round they are literally shooting at you unless you are right next to full cover. (in which case, Reflexes test could see who's quicker).
Question 1 and 2: Firing into an engagement
Bob and Jon are fighting - and moving erratically (3 extra MP for Ashley to pay). If Bob is aware of Ashley and covers part of himself with the shield, he doesn't get to use it to do Block manuevers etc. against Jon. It doesn't matter if Bob or Jon is the attacker here.
Maybe they're by a tree, or a statue or something that Bob could use as cover? Then he can pull some dice and make a Terrain check.
That's it. He doesn't have a lot of options. That said, Ashley will be taking 2-4 rounds to even get the arrow nocked and aiming, plus an average 1-3 more rounds of aiming... if Bob was aware of her and hasn't peeled off a few dice for Terrain to move to a favorable position before that, he's out of luck.
Question 3: When do you declare shots?
After you've got the arrow nocked - once you start Aiming, you declare who you're aiming at. If you stop aiming at them ("a guy jumps out from the side at you!") you lose the dice you've accumulated.
Ranged weapons are really hard to defend against, but also you spend several rounds having to build up dice to even hit someone with.
Question 4: Charging the Archer
Some Dude starts charging Ashley.
1) Is she aware of him? (No? He charges and she either shoots at what she was aiming for or he hits her first, depending on her aiming time, etc.)
2) Is she aiming at him? Then she can start building a Missle Pool.
3) Is he running straight for her, full speed? (Moving target -2 MP). Is he zigzaging, etc? (Erratic -3 MP, but he ends up approaching slower instead of a straight line.) If he has his shield covering a few parts of himself, they count as armored w/the shield's armor rating.
4) It's unlikely that he would be reaching her JUST as she fires, but if so, make a Reflexes test.
They are not engaged in melee until he reaches her. Her Missle Pool cannot be blocked by his Combat Pool or affected in anyway. If he's swinging on her, her Missle Pool cannot block his combat pool, etc.
Pretty much all of the time either the melee person doesn't have enough time to get there before being shot at, or the archer doesn't have enough time to shoot before being rushed. An archer with range and some time can pick off people in a pretty nasty way. An archer getting rushed is in big trouble (suggestion- forget aiming, just go to Evade and Terrain rolls to escape, then pick a new position to fire from, unless you're good with a knife and can get it out in time...)