VPN connections connect otherwise unconnected private networks. The question of what traffic flows over these connections is not generally defined by the VPN tunnel itself, but by other measures such as routing and firewalls.
You can have as many VPN connections on a server as you like. If you want to use a particular VPN connection to send/receive mail, then you need to configure your mail server or client appropriately, but that has got nothing to do with the VPN connection as such. Same goes for IM or any other application.
VPN connections exist at the IP level of networks, they don't interfere with the application layer or other higher network layers. The same is true for routing. As far as I know, normal routing instructions cannot include port definitions or particular TCP protocols. This sort of thing needs to be done in a firewall (e.g. iptables under Linux or whatever you are using) and is usually called port-forwarding.
Whether what you want to do is achievable depends very much on the individual situation. You would need to post more detail before this can be answered.