not real clear what you are saying here but i will shoot at it.
what is your control panel?
for all intents and purposes we will suppose you dont have one and are running ragshod, nothing but the black window CLI ssh.
zip filename.zip directory1_to_add directory2_to_add
directory2_to_add is optional
/site1 /site2
site1 needs to be zipped site2 needs to move to /site1 dir
or
tar -czf filename.tar.gz directory1_to_add directory2_to_add
mv /site1 /old_site_1
mv /site2 /site1
and if everything checks out, u can nuke /old_site_1 later
use zip or tar, not all machines have zip on them, but the larger % have the ability to tar if they are *nix machine
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