You can install Qube's version of MySQL onto the same server, it will run on port 3300, which should not conflict with SQL Server's default port of 1433.
You can also move the MySQL datadir, but since the supervisor installation routine on Windows will always assume that the tables live in C:\Program Files\pfx\qube\mysql\Data\, you must wait until after the supervisor installation has completed. At this point you would need to shut down the qubesupervisor and pfxmysql services (in that order), and then edit c:\Program Files\pfx\qube\mysql\my.cnf and set the datadir variable in the [mysqld] group to the appropriate value.
There will also be a wrinkle when you want to upgrade the supervisor; I'm not certain if the installer will respect the datadir location. You may have to move the MySQL data back to C:\Program Files\pfx\qube\mysql\Data\ to do the upgrade, them move it back afterwards.
