Restoring From Time Machine Backup - HELP!!

HI, I have a Mac Pro running Lion and the main Mac HD drive has just died so I had to reformat it, which was no big deal, as I have a time machine attached. Unfortunately, the time machine was also backing up 2 of the other internal storage bays, each 1.5tb so when I went to reinstal from the time machine, the destination drive (250gb) wasn't big enough obviusly. Is there any way I can direct the restore to a specific backup (ie The original Mac HD backup for bay 1).

Hope that all makes sense, please, any help would be greatly appriciated!!!😕