Leaving the a/c on auto is probably best year-round. First, it should only turn the compressor on when needed, and in defrost mode, it helps to have the compressor on to speed up defrosting. Plus I've always heard that the compressor should run from time to time in the winter to keep the seals functioning properly.
That said, I have my a/c compressor set to the 'off' mode (via the setting in the SID). I press the auto button (or the a/c button) only when needed. I always turn the compressor off every time I shut the car off so the compressor isn't on when I start the car. I once read that its better to have the a/c compressor off when starting the car to reduce load on the starter. Realisticly, I seriously doubt it's that big of deal but it's a habit I've gotten into doing on all my cars. Probably the best and easiest thing is to leave the car in auto and let it do its thing.
In regards to the mudflaps, I couldn't find anything doing a very quick search online but I know I have some old accessory catalogs from 2003-2005 that have them in it. I would imagine the flaps from the Linear/Arc would fit on the 2.0T (I know there are no flaps available for the Aero). I can try and get a part number tonight unless someone beats me to it.