Any battery will get along with the stock alternator, as long as it gets along with the rest of the system (12VDC, and at least 400CCA, IIRC.)
It's also possible to run a pair of 6VDC batteries in series (total 12VDC,) but that gives you potential headaches later.
I'd use an Optima - either a Red top (staring battery with DEEP draw ability) or a Blue(?) top (Starting/Deep Cycle. I think it's blue - might be Yellow.)
However, upgrading the alternator might not be a bad idea if you plan on doing some heavy drawing - not only will the increased alternator output reduce the draw on the battery, but it will also help to charge the battery quicker. Of course, a "high-output" alternator doesn't produce full output until a crankshaft speed of 1500-2000RPM is attained - but that's easy enough to do later.
If you are planning on sourcing a LOT of "deep draw" stuff, it might be a good idea to supplement the starting battery with a deep cycle or two, and setting them up on an isolator or a solenoid so that the deep cycles feed electrical accessories with the key OFF, and all batteries are ganged into the system (for charging) with the key ON.
Batteries in parallel (like poles connected,) it's safe to say that you will still get 12VDC from the stack, but you'll get 95-99% of the TOTAL available current (add the batteries together to figure out what that is) - but it also takes that much longer to charge from full dry (which you should rarely - if ever - hit.)
As far as alternators, click on the link in my sig, and go to "San Jose Generator." You'll have to call him, but he does good work and I'm trying to convince him that there's "money in them thar Jeepers" - so we can get another option beyond Mean Green for high-power or specialty stuff. At least check him out - I've done the site as a favour to him, so you'll have to call him yourself to check into anything not listed.
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