Welcome to FT!
I think you already have a good plan: have one account at each major alliance (AA at OW, UA at *A, DL at ST) and credit the flights there.
Whenever you can influence the choice of airline, steer towards *A. (My primary FF program is at AA, but you said it is not a player in your market.)
If possible work out a deal that you'd buy your own tickets and get reimbursed. Then you can get credit card miles too.
For the hotels, best to join the hotel programs themselves.