There can be a lot of MySQL services in the machine using different ports of the machine so there won't be any problems to have them. The installer checks if the 3306 port is in used at installation time, if it's free, the MySQL service of the new installation will use it, if not, the installer will ask you to select a different port.
In case you just installed the Ghost stack in your machine and you don't have anything important there, you can uninstall it temporarily, start the MySQL server you previously installed and install the Ghost stack again. This time it will ask you to select a different port so you can have your first MySQL server running in the 3306 port and the Ghost's MySQL running in the 3307 (for example). If you already have useful information in the Ghost's installation, we will help you configuring that MySQL to use a different port.
As I mentioned, all our stacks include all the components that they need to run, so it won't break any of your existing services (database, web server, ...) and our stacks will ask you to select a different port in case the default one is currently in use.
I hope this information helps.