You have gotten some great advice and I think you are on the right track.
That said,
*Skip sleeping in the back, 2 full size adults and 2 45lb dogs will be tight AND you will have to unload everything to be able to do this. Its a pain when the dog has to pee early morning (or one of you for that matter)......just buy a tent, they are cheap and its so much more convenient. If I was single I would sleep in the 4runner everyday but not with a spouse, pets and gear
*Try Loading up your stuff and dogs before buying anything. we did a 9 day excursion (camped almost every night) and didn't need a roof rack, trailer or sky box. Unless you are taking lots of activity gear (ski's, bikes, etc) clothes , camping gear and some food will easily fit in the cargo space if you pack wisely.
*If it turns out that you do need all the stuff and it wont fit in the back I would go with a skybox on top. A trailer is an unneeded hassle (my opinion) and a roof rack is a great expense considering its upfront costs and then you still have to buy something to store stuff in.
*Regarding traveling with Pets, I would keep them in the back seat and not lay the seats down. Keeps everything separated and you can still use the rear footwells for storage.