I think a lot of the answers here are way too complicated and based on more advanced trainers using split routines.
The OP is doing a 'BB Beginner Program', so I am assuming a whole body workout three times a week, not a split with a chest day.
I would say Yes you can alternate flat and incline benches on alternate workouts, would probably be the best option for a body building style beginners routine.
If you want do some dips and push ups on your rest days between main workouts if you are recovering well enough between workouts.