Auto clean as far as I know is for dry wall sanding where the vac is used without a traditional bag fitted. Auto clean pops the air filter to shake off the fine filler dust into the bottom of the vac.
I've done some dry wall sanding but have never been brave enough to follow the instructions and use without the traditional bag. Luckily each time I've done it, the bag was pretty full anyway.
Auto clean can be switched off and therefore won't affect its performance on regular wood application.
Only things to mention when choosing a vac- bag size, hose size, and CFM.
My CT36 E AC HD is perfect for everything from wood to dry wall, but is a big vac. I also have a CT Mini I for smaller jobs around the house. I think a CT36 would be ideal for you, make sure it has a 36 hose (you might need an adapter for the domino if it's the smaller one).