I did some more thinking on it and I think I found a good system for it. I would like your opinion on it if it sounds fun and engaging.
So the Fangwood is a confusing and difficult environment to travel through. Because of this, I'm limiting my PCs to three expeditions a week where I'll roll a die to see what event they stumble into next. On the way to the event I'll roll an chance for a random encounter, and on the way back from the expedition I'll roll it again. This way things can happen on the way to a location, at the location, and on the way back from a location. I feel like it will make things a little more interesting and add to the vastness of the Fangwood.
One day of the week will be dedicated to resolving Militia actions, they can do a couple of checks this day, but for the most part they're drilling the Militia, commanding teams, and any other actions the militia requires.
The two other days of the week are personal down time, giving people time to bathe, sharpen their swords, fletch some arrows.
So in theory a week should run like this: Militia, Expedition, Downtime, Expedition, Downtime, Expedition - Repeat.