There's a readme file in the iOOTP2012.app/iOOTPData/logos directory that explains how to add team colors to a logo filename in order to automatically set the colors for any team that gets that logo. Problem is, it isn't working for me - the colors always come out as dark grey on extremely dark grey.
Is the readme accurate? I'm pretty sure I'm getting the color codes right.
Here is the filename I'm using:
Montreal_Expos_004082156_252254252.png
Here is what it looks like:
