So with every WWE game I create a spreadsheet that keeps track of the teams I want to create, feuds, etc. Typically this sheet goes no further than helping me build teams in the game. With WWE 12 though I am now editing shows, brands, etc in WWE Universe Mode.
Here is how my two brands look right now:
Nitro is on Monday, RAW is on Friday and the Thursday show mixes the two rosters. Unfortunately, there's no way to make the Thursday show brand-specific. I typically simulate that show and don't even bother with it. Another minor annoyance is that the game insists upon certain feuds regardless of brand affiliation.
So far though I must say that WWE '12 has absolutely lived up to the hype.