These are the notes for GoZync 3. Docs for the latest version of GoZync--GoZync 4--can be found here. GoZync 4 is a free upgrade and is highly recommended (hint: it's faster).
Does GoZync work with separated solutions?
Yes. In fact it can be quite nice to Zync separated systems as you can use GoZync to deliver new builds of your interface files, clobbering the versions already on your user' device.
Where do the sync layouts go?
The easiest thing to do is put them in the data file. Then GoZync even know your solution is separated and there are no issues.
But, you can put the sync layouts in your interface file if you wish. You'll just need to change two scripts, one in GoZyncMobile and another in GoZyncHosted. You'll find instructions for modifying these two scripts here.