Not sure if it's the same for all MEP versions, but in VPX you just click the top right [X] button -- unhelpfully saying 'Cancel' when the mouse is over it! The changes I made to one of the presets were definitely applied to my audio track and they were still there after I saved my project (new name) and reloaded it.
Thanks Carl. It looks like when you bring up the Mastering Suite, any change you make to the various controls are immediately put into the sound track. It is different from other changes you may make, which give a verification in one way or another. It is off putting the (x) button is the actual confirmation, in a roundabout way. See you.