Tlynn, a few things. One, I don't open any void space without smoking first (no offense Kathy). Smoke the entrance a decent bit, then expose the hive. The bees are the most agitated when exposing the colony, but once its exposed, its all downhill from there. They settle down quickly once they are exposed, and the vast majority 95% or so will remain on the combs or the wall.
Try and use natural light when removing them or a red light, a bright white light they will fly to and you will have a bunch more flying around than you may want. Open exterior doors or windows also if you can.
The one on the toliet, same thing. Smoke them, access the colony, let them settle down, then do your thing.
Take your time, and remove the comb sections from the outside, leaving some in the center. She may run to the outside anyway, if she's a shy queen, but she very well may wind up in the center.
Keep a watchful eye out for the queen but remember, most of the time in a cut out, the queen is found when almost every section of comb has been removed. There will usually be a cluster somewhere, usually at the top corner, if a wall void, and the queen will be inside the cluster.
If you need to talk further and have specific questions you can pm me if you like or Iddee.
...JP