The released version of my Conference Realignment mod is now available in the Download section under NCAA Football for PSP NCAA Football 2007 (PS2 soon). You have to do a lot of manually labor though, so be prepared for frustration!
In the zip will be a bunch of csv files, and a spreadsheet. It also includes an already modded save for NCAA PSP 07. It is unencrypted so you'll need to use PPSSPP to play it and/or save it encrypted.
To mod your own NCAA 06 or NCAA 07 save, download Madden DB Editor 3.0.
Open your save file in DB Editor and for import the csvs into the following tables in your save:
BOWL - Not sure this will work with 06 yet. Study it and modify your own 06 BOWL table!
SCHD - Not sure this will work with 06 yet. Study it and modify your own 06 SCHD table!
Then you need to open up the TEAM table in the editor.
Also open up either STTM.csv or the excel spreadsheet and go to the STTM page. Now you have to manually edit the teams database CGID/DGIDs to move teams around. If you look at the Excel version, it's color coded and sorted already to what it should be. So just look for the red numbers to modify.
Unfortunately, we can't import the csv to this particular table - it crashes.