Don't take this as a definitive answer, but I have multi-aliased CentOS boxen.
I find that outgoing connections always come from the main IP address, not the aliases. In particular these boxen are web servers hosting multiple sites, hence the multi-IP and connections to the database all appear to be from the main IP.
Applications can be attached to individual IPs, but I think the default routing is to use the main IP of the interface.