Customizer Usage in eNewsletter

Sorry this is not a direct support question. I am hoping you can at least steer me in the right direction... I have been working on a plugin in my spare time and when I saw the way eNewsletter uses the WP Customizer it all came clear :wink: I have spent the last few days working with the code etc. for the customizer and it is working great. I have run into a problem though that I can't seem to find an answer to anywhere. I want my plugin to use the Customizer on it's own like eNewsletter does... meaning that I don't want the Current activated themes settings mixed in with my plugin settings (I hope you follow what I mean). I can't seem to figure out how to do this.