I wrote up a blog post on how I managed to get several ‘instances’ of sequenceserver running at the same time for different sets of databases under Apache with Phusion Passenger
http://guy-leonard.co.uk/programs/running-multiple-sequenceservers-on-apache2-and-ruby-1-9/
We have it set up like this as we have multiple genome projects and until they are in draft form / published we prefer to keep them private but have collaborators outside of the lab…
It seems to work! 
Hope it might be helpful for others to follow along…