It all depends on what outputs you're using from the deck.
In the stock JBL premium system, the outputs going to the rear are not amplified yet. They are the equivalent of using RCA cables. When I put my headunit in (before I put the rest of my system in), I modified the amp integration harness by soldering on RCA connectors which I bought at Radio Shack, and plugging them into the preouts on the deck. This worked fine and dandy. If you have it set up like THIS and bypass the amps, you won't have what we like to call "volume". If you instead decide to run the speaker wire outputs from the deck through that same harness, and run to the amps, it will, as Jeremy said, be amplified twice. In which case, bypassing might be a way to go, but I doubt I would. The amps built into headunits are puny and far overrated. I heard from an audio friend that they aren't even regulated like home theater stuff is, so in theory they could say "700x4 power, yo!!!!!!!!!11111".
My 7 cents.