[SOLVED] Thank you for the input. Here's what I did:
I disabled the reaction wheels, RCS ports, engines, etc. on the mini ship in the SPH by default. I set number 6 to toggle RCS, engines, and reaction wheels. This way, I can turn the ship on and off as a whole using one key. I put all the engines of the mini ship in the final stage (which I plan on never using). I suppose stage-lock could be used once launched (Alt+L). I didn't see an elegant way to have staging on the mini ship and still be able to disable/enable the engines and RCS ports.
I removed the gear functionality from the G key on the mini ship (but left the gear toggle for the main ship) and changed number 5 to toggle gear.
Between using numbers 5 and 6, I get the functionality I want and I only use up two command keys.
Another thing to note is that I right-clicked the fuel tanks in the SPH and clicked the green arrow next to the LfOx mixtures to prevent the main ship's RCS or various thrusters from eating the mini ship's supply.
