You are confusing the "Family Bedroom" with the plain old "Bedroom"; they are 2 very different things.
There is one "Family Bedroom" on the lower level of the sleeping car. It has 4 berths: 2 regular size + 2 sized for small children (much smaller than your daughters). It has no in-room facilities. Shared toilets and a shower are down the hall on the same level. The Family Bedroom takes up the full width of the car, with small windows on both sides.
There are several "Bedrooms" on the upper level. They have 2 regular sized berths, upper & lower. They have an enclosed bathroom that doubles as a shower stall. They have a large window on one side; on the other side there is a window onto the corridor which also has an outside window, so there is some visibility out to both sides.
The Roomettes are arranged along both sides of the car, separated by a central corridor. They have an upper and lower berth, with no toilet or shower. There are roomettes on both the upper and lower levels. There is one shared bathroom on the upper level, and several more plus the shower on the lower level. There is a large window on one side, but no visibility out to the other side of the train.
If you want private facilities, get one bedroom and one upper level roomette. You and wife can sleep in the bedroom, and relegate the girls to the roomette -- or vice versa if you're feeling generous. Everyone can use the bathroom in the bedroom if they don't want to use the shared ones, and you can all spend time together during the day in the bedroom, when you're not enjoying views in the Sightseer Lounge. Note that doors on Amtrak rooms lock from the inside only, so the roomette occupants would have to use the shared facilities while the bedroom occupants are sleeping.