what do you mean subfolders for the version? do you mean so you dont have like 15 mods folders that you swap each time you want to play a different modded version?
To answer your question, no I just select the vanilla launcher profile (I do rename every profile) I want to play and go!
My MC mod tree follows:
1.10.2/ 1.10.2 Mods (10)
1.11.2/ 1.11.2 Mods (9)
I most often play profile MC1.10.2F(orge)L(iteLoader)-2185. Much less often MC1.11.2FL-2200, not all Mods I use have updated yet.