i sometimes in this situation....if its a variation on a base design....make 2 copies of the original file and then alter each file so i don't get to mixed up , once i have completed the design changes i have then imported the design layers into the master file and then created my viewports.....i know i am probably doing it all wrong but i find this easier and less complicated.....i just name my files option 1 option 2 and so on..
it works for me but i know it's not the correct way