Yea, you can do that, but being a Jensen 400w 4 ch amp, you'd only be looking at maybe 200w (peak, 100w RMS most likely) going to the subs on that bridged channel. Depending on the subs, this might not be enough to really get any thump out of them.
Personally, I would use the 4ch for all my stock speakers, then get a decent 2ch or mono amp for the subs. You can usually find something cheap on craigslist that will get the job done. However, if you're not looking for serious pounding, I would try the "3 channel" setup and see how it sounds before spending more money.