I can’t really help with your ‘moving Joomla!’ question, as I don’t have a lot of expereince with Joomla!
However, as for where to install software; Since you intend to have the packages on their own sub-domains, I would suggest keeping the web-directories for the sub-domains as separate as possible, ie: not in sub-directories of the parent domains web-directory. This will prevent some problems, such as the interaction of .htaccess files etc.
Joomla -> /home/username/wesowlspta.org/
Collaborate -> /home/username/collaborate.wesowlspta.org/
forum -> /home/username/forums.wesowlspta.org/
and so on…
This is actually the default behaviour when you add sub-domains via the panel, so you shouldn’t have to do much to organise things this way.
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