Well behaved anitvirus programs can safely work together in peace and harmony.
Unfortunately, relatively few AVs are well behaved.
On my new desktop, I’ve got Avast (came with the machine, has a free version, and is a pretty good product) and MSE (it’s free, and it’s pretty safe for most users, although, as a professional, some parts of it irk me). I’ve set both to ignore the virus zoo, although they aren’t too good at taking that restriction to heart.
MSE quarantined a few samples before I got things tuned. Of course, it doesn’t have any function to get stuff out of “quarantine.” (As I say, as a professional this is irksome, but, considering the average user, I’d say this is a darn good thing.)
Today Avast gave me a warning of some dangerous files. They were the ones MSE quarantined.
(In case anyone is interested, the quarantine seems to be in \ProgramData\Microsoft\Microsoft Antimalware\LocalCopy.)