For routes that just change the dialogue and not the ending, all you really have to do is say "this leads to ending B", just write up the changes in the dialogue in it's own section either before or after a key branch event.
For stuff after fights, it depends on if it's different or not, but keep it in its own bracket, thankfully this isn't Blazblue where you get something different even if you LOSE.
For now just
Character A Talking: Blahblahblah
Character B Talking: Blahblahblah
*they fight*
------------------------------
*end of fight between A and B*
Character B Talking: Blahblahblah
Character A Talking: Blahblahblah
------------
Character A Talking
Character C Talking (and move on from here.)
If you get a different conversation because it's a branch arc, then specify this is part of such and such conditions.
If the branch changes because you deliberately LOST, then specify that. Something like *Jam Loses the Battle and Gets Brainwashed*