Matthew,
It’s no problem at all. I must have 6 various combinations of Eclipse / MyEclipse installed on mine. 🙂 Just use seperate directories for each Eclipse installation and seperate directories for each corresponding MyEclipse installation. You shouldn’t experience any issues at all, but DO NOT try to share workspaces between the two. Eclipse 3.0 can read a 2.1.1 workspace, but the same cannot be said the other way around.
–Scott
MyEclipse Support