Sorry for leaving it in a terrible state with terrible bugs and ui, just kinda don't have enugh time for it anymore
In any case, a tileset with "main" checked SHOULD get drawn before any others. The editor for the tilesets is probably not ideal, if you need to change the order you can close gonstruct and edit the preferences file in something like C
Users\<User>\AppData\Roaming\gonstruct (Windows 7).