Install Express/Standard side-by-side
Is there a really good reason you do want to use a shared root directory? From my experience on SQL 2000 and 2005 it sometimes wasn't the best option.   

Having them separate would make it less likely that a change/patch in one might accidentally affect the other or edge cases where NTFS permissions/corruption or something aggravates another issue causing more troubleshooting or affecting both.  If there's not a strong reason to keep them shared, I typically separate due to a tiny amount of bad experiences.