My teams are based together in a realistic pattern. If this causes them to be out of cover, too bad. I've seen some cheesy moves in games where a guy will line up all of the minis from a team to avoid being out of cover. From my experience, it's hard to assist with feeding a machine gun standing behind the guy firing the weapon.... The same goes for my mortar teams.
If you want to use multi-basing for ease of movement in the game, use a skirmish tray. That way you have the benefits of easy movement and freedom to re-arrange the minis when cover is a concern.