I use one template for 99% of my work. I also use a template, matching the GS template, in my sequencer. I save this as my default setup in GS and as my Basic Setup in my sequencer. Of course I have always the same setup for start this way.
If I use a different setup, I save it in GS with a xyz name. When I load GS again, it first will load the default setup.From FILE, I open the xyz file and start my sequencer from GS.I open the midi-file which used the xyz setup. You should have the same settings as you had when you saved.
I used to make a mistake when closing GS, after I made some changes in GS during my work, GS asking if I want to save it, I automaticaly answered Yes, and saved the file I realy did not want, mixing things up for the next loading. Now, unless I want to make the changes to either the default or an xyz setup permanent, I say NO.
I hope this helps.