Yet another SCT Tuner Question

OK, thus far other than a few appearance modifications, my performance modifications have been pretty much non-existent. I've only added Flowmaster axle backs (which is basically for sound only) and a BBK CIA. After some debating, I've decided that my next modification will be purchasing an SCT Tuner (either the xCal 2 or the xCal 3) and a set of FMS 4.10 gears. Not knowing a lot.....make that knowing NOTHING about computer tuning a car, I'm not sure how it all works. My plan is to order the SCT tuner the next week or so, then add the gears some time in early April. So my question is, can I add then tune to my car now and then change the gear ratio in the computer with the stock out of the box tuner? Will I need a custom tune for the gear? What all factors do I need to consider? Any help from anyone would be most helpful.

So since I have the BBK CIA, would I benefit from a custom tune? The main reason that I went with the BBK in first place was that I couldn't afford both the CIA and a tuner at the time. And since the BBK didn't require a tune, as well as me not being familiar with tuners, I went with the BBK CIA. If I purchase the Tuner from Brenspeed, will it be loaded with generic tunes or will it be loaded with a tunes tuned by Breenspeed? This is where I get a bit confused.

kooldawg6, thanks for the info man. Now that I have a clearer understanding, I'll be ordering my tuner from Brenspeed tomorrow.