1. I switched from my star cruiser to my shuttle craft and then back again and it messed up BOFF assignments. Is there any away we could save our different BOFF assignments for that ship?

2. This also could be used for selecting a different battle template or another within seconds.

Nope, always have to re-assign. Hoping for an option at some point. Doesn't take long or much effort to get them back in their spots, but still a bit tedious and shouldn't be necessary.