I don't know why you'd want to have to have multiple src trees (cross-compiling for another system?) But you shouldn't have to chance the base. inside /var/db/sup is a checkout file. Mine ends in RELENG_8 (8.0-STABLE, which I run.) I imagine it'd generate a second file if you supped HEAD.
I don't know about how well the src would divide in the /usr folder though, you might have to set two different prefixes (although I don't know)
ports also won't matter here because you'll want to be tracking HEAD for the ports tree. When you specify anything else (e.g. RELENG_8_0_0_RELEASE) you're getting the ports tree as it existed when 8.0-RELEASE was frozen to be put on CD/ftp for distribution.
Going to need someone else to comment on the /prefix with two src trees though. I've never done it :P I've never tried to cross-compile a different version of FreeBSD.
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