Particularly if cost is an issue, you either need to learn to work on this thing yourself, or find a good honest shop to maintain it for you. Or more likely, both. If your dealer has a good repair shop, that's fine, but often there's a better option.
Asking for a recommendation in the forums can be a start, or you can look in the yellow pages for auto repair places that specialize in VW/Porsche/Audi. Find out if there's a VW/Audi club in your area and see who they recommend.
It's not really worth much to have the dealer enter the radio code, since the directions are in the radio manual. Throttle plate adaptation is also easy. If you think ahead about this stuff, a set of jumper cables can make it so you don't have to do either one.
If you're going to work on it yourself, you may want to get a Bentley (shop manual) and a VCDS/Vag-Com (computer interface) if you don't have one yet. Part of the basic toolkit required to work on these cars.
Don't get scared, it's just a car, but there are right ways to do things that your average mechanic isn't going to learn about by working on American or Japanese cars. You don't want the mechanic to get his training by trial and error on your car.
$250 for a battery seems like an unnecessarily expensive first step, particularly if it's the alternator that's the problem, which is likely. Check into having a reputable local shop rebuild your existing alternator. Sometimes it's a cheaper alternative, and you know you're getting a real OEM part back.
I still recommend starting with the cheap stuff and working your way up instead of parts-swapping until it goes away.
Don't take this the wrong way, but if you can't afford to (or don't want to) maintain this car, you should get rid of it. Cheap to buy, expensive to maintain, especially if a previous owner skimped on maintenance. It has expensive systems that will eventually fail, and they'll fail sooner if you can't afford to maintain them on a regular basis. Driving with failed air springs will do more damage. Skipping the timing belt service can require repairs that cost more than the car is worth. Ditto for using cheap oil. It has a high-strung motor in a complicated car with an advanced suspension, and even if you got it cheap off the used lot, it's still just as expensive to maintain as it was when it sold for $50,000 or whatever it was.
Ok, I'm over it now.