I just started running this game for some fun, but I don't know if I have to do some configuration stuff for the steam version. A lot of people mention a DRM free version, and completely restarting the game by deleting the files in appdata/local or whatever, but when I do that Flowey still knows that I "accidentally" killed Toriel on my first playthrough (For the record, I didn't think to just try and spare her over and over again)
Any help would be appreciated.

Also, I think people run it in the [old_version_100] mode, but my game crashes on startup when I do that.

The best version to run on is the linux version. you don't actually need linux to run this version, we ported it to windows. instructions on it here: http://www.speedrun.com/undertale/thread/gvkrv

You will need to disconnect the game from steam, by going into the steam folder the game is stored in (location is mentioned in the link i posted before) by deleting steam_api.dll and moving all the game files to a different location and running the game from there.

if you haven't disconnected the game from steam, steam will load its cloud sync every time you open the game, even if it's disabled.

Thank you!