Does GoZync work with separated solutions?
Yes. In fact it can be quite nice to sync separated systems as you can use GoZync to deliver new builds of your interface files, clobbering the versions already on your users' devices.
It doesn't matter where you put the scripts and layouts you'll add to your hosted file--you can add these to the data file or the interface file. You may want to put the code in your data file if you have only one data file as that would mean you could sync without opening your interface file, which is undoubtedly faster. If you have more than one data file you'll want to add these scripts and layouts to your interface file so you can access all your data files from one place.
In your mobile files the work is done in GoZyncMobile so there are no layouts to add; the scripts you add are interface-type scripts (the scripts for your sync buttons, for example) and those belong in the interface file.
GoZync's required fields don't need to be added to your interface tables, just to tables you want to sync.