If you both try to select a vehicle to steal that your partner already has marked, the game will tell you that it's already in progress. I got credit for 2 or 3 that my buddy was working on halfway across the map, simply because I was working on a different target. It doesn't seem to matter if you've got the same one selected, so long as you both have one marked.
Assassinations count for both people, if you both have any target selected.For example, if you want the bonus for owning a store, you have to buy that store. Challenges in the Saintsbook and controlling parts of the city are determined separately, co-op or not.Activities and other side missions count for both people if finished in co-op.If the mission unlocks something (ie, a new crib) you'll have access to this in your game, regardless of whether or not you've gotten there yourself. If you finish a story mission in co-op that is ahead of your own story process, when you catch up (in single player or if you're the host next time) you'll have the option to skip this mission.
I did some research and asked the guys I co-op with.