Agree with Nos - keep your options open.
If your aux is only required for emergency back-up power, then I'd be inclined to have a separate source of fuel for it. Perhaps a 3 gal plastic tank will do the job?
If, on the other hand, you intend to use it more for everyday low speed stuff, you'll probably prefer to run it off the main tank with a T piece or changeover valve in the fuel line.
Carrying spare fuel on board is a bit of a PITA when you already have a large underdeck tank, but if your main fuel supply becomes contaminated, will the integral/separate tank of your aux have enough capacity to get you home?
You can get changeover valves from Pirtek, ASAP Supplies, Aquafax, etc.