1.) You bring it into a APR dealership. Around here, some of the APR dealerships are also VW dealerships, so it works out warranty wise.
2.) Are you asking that you want a totally new ECU and then put the stock one back in for work? That's involved and expensive. If you're that worried about warranty work, then see if there's a mod friendly dealer around or don't get flashed at all.
3.) APR has the EMCS system that you use through the cruise control. You basically hold down the set button and the CEL flashes once, that's program one, usually stock. You keep holding it down, it flashes twice, that's program 2, usually 91 or 93 octane program.
BTW, APR has their sale till next Friday where if you get the one program, you get another one free ($150 dollar value) AKA you buy 93 program, you can have stock programming for free. If you buy 2 programs for $750 plus tax and labor, then you get a fully loaded ECU (Stock, 91/93, 100 octane, etc etc.); everything but the security lockout which is another $60 if I recall correctly.
I'm pretty informed about this stuff and I don't even have it yet. Got to do your research man.
It's literally all on their website, except the sale pricing.
http://www.goapr.com/VW/products/ecu_upgrade_mkvgti.html