We did a similar trip to Manilla last summer. We didnt rent a houseboat, but the marina at Manilla rents a "floating cottage" or something like that. Its an old houseboat that has been pulled into a slip in the marina and tied to power and water. They pulled the helm and engines, but everything else is the same. The "cottage" came with the slip next to it, we we launched our ski boat and left it tied on the other side of the dock all week.
The campsite at the marina is very nice too, we had some family stay in the tent sites there. Bathrooms, showers, covered patios, etc. Their tent site was right up against the bay around the corner so they could even walk to the water. There wasnt much sand beach when we were there, so we didnt anchor by them, but we picked them up a few times.
As far as good places for water, I wasnt able to find glass water in hidden canyons like you can in Powell, but after getting far enough away from the marina we always ended up with water that was plenty good for our needs. Flaming Gorge is great, youll love it. Its similar to Lake Powell, but different, its a different kind of pretty. We usually ended up floating through horseshoe canyon at least once a day. Its a big horseshoe off the main channel, a few miles long maybe, but the whole thing is wakeless so its just a nice mellow float. The exit is just about in the spot spot the entrance is in the main channel, so you dont need to go back through the way you came when you return.
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