Whenever I have a game that has different routes/paths, I usually do it the dumbest way possible: I pick a page, click on the page name and Name it "Rose Path" or something like that. And save the content there.
Like this:
	
		
			
		
		
	
View attachment 1439779
	
		
			
		
		
	
Some games don't have a decent Gallery (or any at all). In these cases I usually save each scene in a separate save file. So in this case I would skip a bunch of pages, to leave room for the scenes of a path, before creating one for a specific path/route. 
This game seems to keep all the scenes, so in theory it shouldn't be necessary to save the game for each scene.
Plus, 
apparently, if you unlock the character, all the scenes you have unlocked in a different save are already available/replayable on the MC's PC. Unless it starts to filter out scenes based on routes, which hasn't been done so far.