Wow, how many questions?! (lol)
1) We book with whoever is offering the best deal! Last couple of times it has included free
DDP - 2007 was with Thomas Cook, - 2009 after booking with Travel City Direct and losing the holiday, we booked flights direct with BA and accomodation direct with Disney UK, both online.
2) Get Disney tickets with whoever accomodation is booked with - need to, to qualify for free DDP. Normally surf the net for best deals for our Universal tickets.
3) tough question - do you want to do it all? Is everyone in your group into fast rides? We are a family of 4 - have the Disney ticket for duration of stay and then 3 day tickets to Universal - have one/two days away from it all e.g Space Kennedy Centre, beach, Converse shopping etc. Have done SeaWorld once with our boys, although they thoroughly enjoyed it in 2003 (their first trip), they have not been overly interested in going back. You can get the Orlando Flexi ticket that will get you into SeaWorld, Wet'n'Wild, Busch Gardens.
4) I personally would stay in one hotel, I couldn't be bothered to move - I figure you would lose best part of a day to pack, move, unpack etc. If you have a car, it's not really that far to other places. There is the benefit of staying at a Universal Hotel - you get free front of the line passes (you still have to pay for entrance). Last few times we have stayed onsite and would do this again in the future (just have to work on DH!)
5) Disney Hotels give you free transport to Disney parks. If you stay onsite, but decide to drive yourself, then you don't pay for parking at Disney parks. In 2007 we had a car that mostly stayed parked at the hotel - just used it to and from the airport and Universal. This year we used ME to and from the airport and Disney buses (Have read bad reports on them, but can honestly say never waited more than 10 mins for one - normally less) - we hired a car for the middle 7 days which enabled us to stock up on water, coke and beer from the supermarket as well as get us to Universal and St. Petes Beach. Haven't used taxi since 1990's, struck me as expensive and driving is a pleasurable experience!
6) As a family we love rides, so always do Universal - a day in each park and then split the third day between the two redoing our favourite rides. MK, DHS, EPCOT, Blizzard Beach and Typhoon Lagoon are a must for us two - always start and end the holiday with a Disney park.
7) Can't really comment as family of four, but OKW do have 2 bedroom flats.
Happy planning.