| FWIW:
A JJ is about as good as config for versatility as any.
Personally I'd run an existing pup straight to the jack (bridge if you're a bridge player, neck if neck, both if you play a lot at the detent) to get an idea of what the pup(s) really sound like and what part the pre/harness is playing in the mix. You may find the tone you want in simply doing that and running controls off the amp.
If tone doesn't seem up to snuff then pups would be my first transplant. Most onboard pre's are pretty transparent and really doesn't make much difference which one you use unless they have some bell or whistle that gives them an edge controlling frequencies. I definitely wouldn't change them both at the same time. Not only would you not know what altered your tone but you may find you don't need to change the pre at all.
Some pre's can be tone-suckers but it's a trial and error thing. Never had an Audere so can't speak to it. The Barts, Aggies, EMG's to me are all basically in the same boat with the choice dependent on things like size, price, whatever. | 
