You can't have a mix of 360s and V6s, all boxes have to be converted together.
I would also look into the differences between the boxes, if you record a lot the V6 has better features in that regard, the 360 is more focused on streaming.
Some of the missing features are as follows; Wishlists (where you can set the box to record programs on certain subjects or featuring certain people), undelete, series link+, series link manager, suggestions, setting of series links for programs not in the current TV guide, ethernet control, keyboard support via USB, switching between tuners with constant buffering, skip-back on fast-forward, quickplay, default recording options, cancelling individual recordings from a series link, multi-channel series links, radio channels allowing recording of radio, separation of recordings between boxes, watching recordings when internet is not available and probably a few others I've forgotten.
Also, extra boxes do not have their own hard disks or tuners (unless converted from a V6 box), so you lose storage space and recording ability and are also reliant on the main box being on to watch and set recordings and also on having a decent wi-fi signal (or ethernet cable) between the two boxes when watching recordings.