Even though it's a system I grew to like slowly (see my question Apocalypse World without Fronts: Are we missing out?) I recommend using something like Fronts from Apocalypse World and Dungeon World for keeping track of things, and keeping it simple. This is my personal adapted version from the core system. It's a reasonably generic system, but I think it's best suited for situations where the antagonists have the initiative most of the time in the grand scheme - luckily, that's a common state of affairs in RPGs and fiction in general.
Fronts (or "Story Arcs")
A Front is defined in Apocalypse World as a set of linked threats and actors, but I prefer to think of them as story arcs. A civil war between the Oompa-Loompa peasants and Uruk-Hai burghers is a Front, with its threats and actors being various political and military leaders, along with their armies, forts and weapons. The Vizier's plot to overthrow the Sultan is a Front, with its actors being the Vizier, his co-conspirators and the Sultan himself. You can include stuff other than characters too: items, locations, enchanted snowstorms etc...
Start by naming a Front, describing what's at stake and listing its most important characters and objects along with short descriptions. These are for the GM only, so you can include stuff your players shouldn't know, but if you want you can create a journal similar to this for the players to remember stuff with:
Vizier seeks Sultan's Throne
Stakes: If the Vizier succeeds, the Sultan will die, and the realm will be ruled by the Famine Cult using the Vizier as their puppet.
Actor: Vizier Rahman craves the Sultan's power, but doesn't have the courage to assassinate him himself. Rahman is secretly a member of the Famine Cult and has basic knowledge of mystic arts.
Actor: Sultan Harun is the young, inexperienced but just ruler of the realm. He is of trusting and gentle nature, and many consider him to be a bit weak. He seldom leaves the confines of his palace, but often meets envoys in his throne room.
Actor: Mistress Fatma is the Sultan's closest servant, and is in charge of all the lesser servants. She knows all the rumours around the palace, has eyes about everywhere, and while she doesn't personally care for the Vizier's attempts she is easily persuaded by gold.
Actor: Sinuhe the Surgeon is the doctor in the town. He's a foreigner but known to be talented, so he'll likely treat the Sultan in the event of any medical emergency.
I recommend keeping the descriptions brief: as you can see, a sentence or three is enough to spell out quite well who's doing what in this situation! Also, it doesn't have to be just characters:
Location: Sultan's Palace is luxurious, known for having a lot of meandering corridors to make it seem larger, and has a huge garden, with secluded pavilions and secrets lying around.
Group: Palace Guards are numerous (a couple of hundred or so) and patrol the Palace and the grounds constantly. They wield deadly but ornamental sabres and wear fancy helmets that obscure the facial features of their wearers.
Object: Sultan's Porcelain Dishes look pretty normal, but are powerfully enchanted to turn bloody red and scream if poisoned food is put on them. Only the Sultan, Fatma and the Vizier know of the enchantment.
And so on. That's a very short description, but tells a lot, and it doesn't have to be 100% comprehensive. If your players show a keen interest in exploring the intrigue of the Famine Cult, you can add them as a Group, writing down a short description for them too. Or if they decide a foreign envoy at the Palace is the most suspicious one, give the envoy an entry to flesh out her character and weave her into the plot. And of course, should someone die, you can draw a little tick next to their name to signify their demise.
Countdowns: Keeping track of ongoing evil
Or "ongoing events" if you prefer.
So now we've got bookkeeping of things in order, so let's move on to events, evil plans and the like. Apocalypse World has this thing called "Countdown" which is a six-phased "doomsday clock" for various bad stuff - or good too, in theory. It is used to remind the GM that there's things about to happen - and these things will inevitably happen without player intervention. Use these for evil schemes, oncoming disasters and so.
A countdown has six phases. For the first three phases, the event is oncoming, but is not certain to happen. The last three, it's already on its way, but there's time to brace for the impact and prevent the worst. At six, the full effect of the event happens - the bad guy casts the spell he's prepared, Sauron forges the One Ring, the planets align to awaken a sleeping god or so on.
An example of such event would be the Vizier from our previous example trying to bribe Mistress Fatma. Draw a six-phased counter or a progress bar, which you will fill up as his attempts proceed. The first three steps represent the Vizier courting Fatma with gifts and trying to gain her support. The players don't get to see the bar - they see Fatma wearing more expensive jewelry than usual, wandering into her thoughts more than usual, having private conversations with the Vizier more than before and so on. Fill this progress bar as time goes on to remind yourself that this is an ongoing situation, and the PCs don't have a lot of time to prevent it. Stop filling it if the players keep investigating the matter and actively hurting the Vizier's actions.
When the progress bar reaches its midpoint, Fatma has agreed to participate in the murder plot. She's still making arrangements, procuring tools for her deed and planning, but she's already committed. The PCs will see her acting weird, may find items in her possession she shouldn't have, may get attacked by her if they dig in too deep. And should the progress bar ever fill up, she'll carry out her plan and attack the Sultan.
Of course you'd want to have more than one countdown to represent such a complex situation of court treachery, where the perpetrator has multiple avenues to pursue their objectives and the Sultan is a bit of a wild card too. I usually list them in a format like this:
Countdown: Vizier bribing Fatma
0-3: Bribes have been delivered
4: Fatma accepts to join the plot
5: Fatma has a murder weapon
6: Fatma carries out the deed
Countdown: Vizier uses poison
0-3: Vizier Rahman is looking for identical non-magical porcelain to replace Sultan's dishes
4: Dishes found: Rahman is procuring poison
5: Rahman has acquired the poison and the non-magical dishes
6: The Sultan is served a poisoned meal
Countdown: Famine Cult wants Action!
0-3: The Vizier is exchanging letters and meeting spies of the cult
4: The Famine Cult decides to off the Sultan in an armed coup
5: The Famine Cult has an armed force ready to act
6: The Palace is assaulted by the Famine Cult
Countdown: Sultan disapproves of paranoid adventurers
0-3: Kind requests to tone done the suspicion
4: Sultan assigns a nosy guard to follow the PCs around
5: Sultan requests the PCs stay in their guest chambers or leave the Palace
6: PCs are thrown out of the Palace
Each countdown reminds you, the GM, of what's going on and, in their "6" phase, what's going to happen if the PCs don't prevent it. Create new ones as you feel appropriate, and strike out ones that have served out their use (for example, the Vizier's death would nullify many of these countdowns).
In a nutshell
- Create a new Front to describe something important that's going on
- For each Front, list what's at stake, important characters, locations, items etc along with short descriptions
- Add to this list when something becomes significant
- Create countdowns that represent events about to unravel
- Keep an eye on the countdowns when GMing, advance them if the fiction warrants it
- Strike out any countdowns that have served their use
- Have fun
For a complete, immersive campaign, you'll probably find yourself having multiple fronts, each with their own actors, and multiple countdowns for each. I advise you to start small though and try to use only one Front at first to get a hang of the system. Also, if you find there's something bugging you with the system, tweak it, adapt it, twist it, cut it. It's meant for you to better manage complex fictional universe storylines, not just to be a series of hoops for you to leap through. Make it yours!