Is there a reason I cant use 2 installations of Joomla on the one site?

root installation for Joomla/community builder "Staffy site content".

subdomain shop.root for Joomla/Virtuemart.

As I cant have integration and will have to use to different applications to handle content and shopping, can I at least stay with the same CMS. I'm thinking of a stripped out shop installation just for vituemart.

Does using a subdomain cause issues down the track.

Hmm - I think it's fine - just be clear on what is a subdomain (needs a record mod, I think) and just a subdirectory. To get yoru paths corretc. You can put a second joomla in a subdirectory no worries etc - joomla is just a web directory you can drop it anywhere you like - just need to make sure paths are corect - I don't quite follow your paths above - but if the 2 sites are separate - but want to look related I would name one - yoursite.com
and the other shop.yoursite.com - and just be careful with paths when linking back and forth and be aware that usign an inetrnal backup liek joomla pack will only back up each individual joomla installation etc.