I've taken the middle seats and table out, so most of the time it's in kombi configuration, albeit with the bench seat on rails. If it's just me, carrying one bike, I'll have the seat forward and the bike crossways in the rear footwell. Front wheel turned at 90 degrees in the side door step. I can get an XL 29er in like than as well.
For carry more bikes and people, they go in the 'boot'. Upside down, wheels off and bags packed between them. Not ideal, so I'm going to sort a better solution. I have been intending to try my Thule Pro rides in the rails, but haven't got round to it yet.