Upgrading is easy. You can use your distribution's üackage manager and simply install the newest available MySQL package for your distribution (but make a backup of your system before). If you want to use two different versions, you'd have to install the second one manually (you cannot use your distribution's packages for it) and configure it to listen on another port than 3306 (I assume your first MySQL version is listening on that port already).
Thanks I had a go last night, but managed to mess something up so that the client sites couldn't use the mySQL. This morning I've donw a complete rebuild, and installed mySQL5 before I installed ISPConfig, and that seems to be working fine. Only thing is now when I reboot the server, ISPConfig asks for a Pass Phrase when it starts apache, and the system won't work unitl it's entered. Any idea what that might be? BTW I'm running Debian (Sarge) PHP5 and mySQL5
Forget That, looks like I was on autopilot this morning and didn't do the reinstall quite right. Fixed it using the code given by Falk here HERE Cheers