Rebel Ops are the green side missions required to level up rebel skills while missions are the obvious story missions.
You might be confused at some point why you ran out of side-missions for 1 area when the map tells you that you still have some missing - that's because they're all connected and certain ones won't spawn before you complete the ones in one of the 2 other areas.
Make sure to immediately complete all tower-defense ( or whatever they're called) side missions to re-unlock the ability to call in a heli. They might be intimidating at first, but the AI is so beyond broken that you can start the broadcast, go prone at the top of the staircase of the tower and sit out the 3-4minute counter. Occasionally someone might peak in or a sniper somehow finds a way to aim at you, but you should be able to deal with that.
The CAL50 is given to you as part of the introduction-story-mission and should always stay equipped as it oneshots Helis and 1-3shots every vehicle. Both things you'll encounter quite a lot in this DLC.
The only frustrating side-missions are the VIP-extractions. As a rule of thumb, the second you talk to the VIP the game will start spawning enemies and at least 1 rocket-heli. Get rid of the later ASAP and kill a huge portion of the enemies before leading the VIP outside. It's best to put them in timeout somewhere in a corner where they can't get hit by explosions.
I'd recommend to sync your save both before the final mission AND save a headhunter-side-mission as your final requirement for this cheevo.
As every other Ubisoft game released in the past decade cheevos are incredibly broken in this one and will often not unlock when they're supposed to. And at least judging by the one that's tied to finishing 1 final rebel op, once your save is screwed, it's screwed and there's no way to unfuck it except deleting your local save and repeating the task.