I follow the same routine for both bally alpha and wms games. After doing a clear and letting the game load, I always follow this pattern.
1. Set clock.
2. Set devices (usually just bill validator, button panel type, and ticket printer)
3. Set denomination/credit
Here I set the denom to $1.00 so the counters don't go too crazy, then I either enable/disable multi-denom depending if there's a progressive.
Select the game percentage and save for all paytables.
4. Set game options (i.e. max bet and button panel layout)
5. Set your progressive if needed.
6. Set your comm for TITO if needed.