In your C:/Papyrus/NASCAR Racing 2003 Season/series folder, find the mod you want to run the season with. Go into that folder, and find a .ini file. There should be at least 2: all.ini and 2003season.ini. Open one of these, you probably want the 2003season.ini (the file opens in either Notepad or Wordpad) and find the race(s) at Bristol and Darlington. Edit the line beginning "trackDirectory =" to have the name of the folder inside your tracks folder where the track you want to run is located (for FSE's Bristol Night 2012, you'd edit the line to read "trackDirectory = Bristol Night 2012 FSE" without the quotes). Save the .ini file as anything you want (if you don't mind overwriting the default 2003season.ini, go ahead and just hit save). Run your season, you should be good to go!
If you want to make a .ini file from scratch, this program NR2003Editor has a fast way to do it.
You don't have to replace the old one's if you wanna race both versions old and new, you can add a new block e.g. copy one from any track and insert it anywhere, edit its info (don't forget to edit the event numbers)