But how would it know which path I chose?
All those things are managed by which quests you complete. It's been a while since I've used the set stage command to move a quest along, but basically you are just telling the save file with a console command to tick off the little mark that a certain point in a particular quest have been done. The game then removes or adds whoever it needs to, changes things around that should be and basically acts just like you really did those quests, with the exception of not killing people/removing things that aren't removed by quest script.
Maybe someone who has used the command more recently than I have can give you a better example. I do know that you can completely rebuild your character *exactly* as they were, as far as skills, stats, gear, very easily. It just takes the form id#s from the geck (you can find them all on the wiki also) and a little bit of typing. I'll walk you through it if you want.
-gunny out.