First you assign the wrestler to which ever brand you want. Next you need to make sure the stats of the wrestler are 85 or above, this will keep them in the title chase (usa title /ic at least). Universe picks stars randomly, so if they turn up is a bit of a needle in a haystack.
For example Evan Bourne of all people won the money in the bank, cashed it in against BATISTA!!!??!??! AND WON! Anyway, .. I digress, after that Bourne lost the title, but was never picked to be a main event-er or even a mid carder. So there doesn't appear to be any logic to how the game picks.
The best thing to do for now, is to have your wrestler perform on both raw and superstar (or smackdown if he isn't on raw) and beat everyone, eventually you will receive a number one contendors shot. After that just let the game take over, the wrestler should stay number one contendor for a long time.
Also if you have any stars you don't want in raw and smack-down, send them packing to the independents ;) As much as I love some of the legends, having Jimmy Snuka in the title chase everymonth does not make me a happy panda.