Each iClone version until now has had its own directory setup, so the same can be expected for iClone 6.
Different versions of iClone can coexist. I have currently IC4 and IC5 installed. Especially in the beginning it is useful to have an older version around.
I have my iClone content on a separate drive and it works fine. As rampa mentions, you can set the location during installation. Changing it afterwards is not completely impossible but requires a registry setting, so it's not recommended for most users.