When doing an exercise with the goal in mind of doing 5 sets per exercise, are those 5 sets for the muscle or for the exercise? Meaning as follows; if i want to do both flat and incline bench presses do I have to divide them so that they equal to 5 sets, or can I do 5 sets per EXERCISE which would result in 10 sets for the muscle?
I'll assume your goal is to gain strength, and that each set is 5 reps (a reasonable number of reps when focusing on strength gains).
If you do 5 sets of 5 reps each on the bench press at a weight that lets you do another 5 sets of 5 reps each on the incline bench press, you're not lifting heavy enough to stimulate the quickest strength gains. You'd get more out of your time at the gym, and make quicker strength gains by lifting with heavier weights, such that you can just barely finish 5 sets of 5 reps of the bench press, and that's it. (Some programs say lift even heavier so that you can only do 3 sets of 5 reps, and leave it at that.)
3-5 sets of 5 reps on bench press is sufficient stress to stimulate adaptation so that when you do it again approximately 4 days later, you will be able to lift a few more pounds.
When people talk about sets, they're talking about sets per exercise. But, when you set up your program, that should be synonymous with sets per muscle group, but don't split those sets between two exercises that are so close to each other as the bench and incline bench. Rather, pick the bench as your main chest lift, make sure you also include overhead press in your programming for your shoulders (on workouts alternating with your bench press workouts), and only do the incline bench press if it's really necessary as an occasional light assistance exercise (since all the muscles worked by the incline bench press are worked sufficiently by the bench press and overhead press).
When describing exercise routines, people are referring to sets per exercise.
But flat and incline bench have enormous amounts of overlap, so doing sets of five for both will mean that you are almost certainly shorting one or both of them with regards to maximal weight, meaning you will build bigger muscles but get strong less quickly. Picking one or the other--and perhaps alternating it with overhead press--would be superior for the goal of strength.