Ive been looking at each factions' flagships and i had an idea to use the lt.com and ensign uni boffs in a creative way. Since the ody is more tank than dps u could use the lt.com as a sci spot and the ensign as a tac. For the bortasqu since its 50/50 go with lt.com tac and the ensign as an eng. Finally the scimis go with lt.com eng and ensign sci.(note:with the scimis it is intended to try and be an alpha strike ship)
Or since this is a dakka based PvE game... you can put the LtCmdr on the Oddy to tactical... the Bortasqu kills things already so it doesn't need help, and you can put the LtCmdr on the Scimitar to Tac and the ens to Engineering.