To directly answer your question, the MS should drive the injectors directly if they are high-impedance. If they are low-impedance, you'll need a flyback circuit as outline in the MS manuals.
I'm not an Audi owner, but I do have Megasquirt on my e30. I did a little Googling to see if anyone else had a similar setup, and I see from your threads on other forums that you're trying to get an increase in gas mileage, and to avoid having to replace your AFM?
My honest advice to you is to banish all thoughts of a standalone conversion from your mind. Get a second, more economical car if you wants more mpgs, and get a junkyard or used AFM. You would more than likely end up needing a second, reliable car if you tried converting to Megasquirt anyway. It's worth it, but basically turns your car into a near-endless project unless you're a wizard with electronics and EFI theory (in which case you wouldn't be asking).
Sorry to be negative, but I wouldn't want you ending up frustrated or carless. If you do get a second car and MS and do your LPG conversion, post up about it!
Also, if you are determined to go this route, www.msextra.com
has a great support forum and probably some similar Audis.