Originally posted by Twoflower
Yes, they are definitely compatible. The problem about it is a bug in the moddir feature that Paradox doesn't seem to be able or willing to fix. Due to this bug, all the mod's scenario files (e.g. 1419 - the Grand Campaign.eug and 1520 - the Age of Reformation.eug) need to be copied from the mod's scenario folder (e.g. EEP\scenarios or AGC\scenarios) to the regular EU2 scenario folder. After that, MP should work fine. I can't make any statement on how stable the mods except EEP are in MP, though. The only thing I know of - having played EEP MP for several months now - is that EEP MPs works hardly any worse than vanilla EU2 and is definitely worth a try.
EDIT: Could some kind mod perhaps make a stickied thread either in this or in the MP forum with the instructions on how to make modifications using moddir compatible to MP?