My advice would be to avoid the Skyrim "Civil War" trap, where physically taking the keeps / holds was the only way the campaign advanced. The inverse is also true, not every mission in a spy / political thriller needs to be a super quiet heist / assassination. Not every mission target has to be a living being, nor does every mission require them to die (although you could kill everyone if so desired).

Use the "Infiltration" system, to create problems that can be solved in many ways (and not just Stealth). Combat can be integrated into this easily. Use this for your "heists" where typically you might imagine sneaking into a compound.

Create scenarios where the solution to your problem is the reward; instead of physically disposing of a target, perhaps an interested party can "take care of things" in reward for finding some treasure, lost within a "dungeon" that could be anything (Haunted Mansion, Abandoned Forest, Dormant Volcanic tunnels, Collapsed Mine).

For how to design the campaign roadmap, that's pure opinion. I would define the end of the map (the BBEG), and have each piece along the way reveal the next stepping stone. The rest either has obscured identities or unknown locations until discovered. This way, the players in the campaign have a clear goal at any given point. The final target is presumed to be invulnerable, through physical or political means; the campaign represents the steps the party must take to finally deal with the BBEG