When I run Wandering Heroes of Ogre Gate, I give the players freedom to move around as they wish, trying to keep things open. I also pay attention to my NPCs and to the different organizations like Martial Sects, who react to things the players do. Between sessions this is fairly easy to track and think about, but during play, keeping dibs on NPCs as they move around and react to what the PCs do can be tricky because your focused on so many things at once. Here is an approach I've drawn upon to help manage that task.
It is pretty straight forward. Basically I print a copy of the setting map, in this case my rough sketch of the Banyan Region (we should have an official hex map in the next few months). Then I use tokens to represent major NPCs who are currently working with or against the party (or who may just be involved peripherally). Right now I like d6s because I can rotate them to indicate how many people are in their group if they have followers or hired thugs (if I need bigger number I can always use d20s or d100s). Then I put a little post-it flag on the dice so I know which individual or group they each represent.
When the session begins I place the dice on the map based on where the NPCs or groups are at that time. As the session progresses and players do different things, I may move them around while they react to what the party is doing or work to take action against them. For example if the party is heading north to find out about the Phoenix Crown from Heiping Sect and they are in the southern city of Chen, I may move Dancing Hawk toward the Redi Pass where he intends to ambush them because he has a grudge (provided he has word of their movement). I might also move Little Venom (who is working to find the crown for The Mystic Sword Sect) to Zun City because she intends to infiltrate the party and thinks they will be passing through that area.
I find this is helpful for a few reasons. First it allows me to plausibly chart the movement of the NPCs. For me this helps with fairness, because I am not magically allowing them to catch up to the players if it isn't feasible for them to do so. It also gives me a better sense of the setting as a GM because I am physically moving my NPCs around. Second having the key players on the board in front of me, but away from my notes, helps remind me to bring them into play when they are relevant. It is easy to forget about this sort of thing, but when you have the tokens in front of you, you are more likely to remember these details. Third it helps me keep track of where everyone is. This is useful because it can swing the other way around. Player Characters might want to track down Dancing Hawk or Little Venom for their own reasons. When I know where the important people are, that is easier to respond to. This also makes it easier for me to get in the head of my NPCs and see what options are available to them.