The embryos should be washed slowly through and ethanol series. We use 25%, 50%, 75% (diluted with PBSTween) and then 2 X 100% ethanol washes. At least 15 minutes at each step. You can then transfer the embryos into the BB:BA.
We embed the BB:BA cleared embryos on slides in DPX solution which allows you to manipulate the embryos and then can be left overnight to harden before imaging. When transferring the BB:BA cleared fish onto the slides you want to try and transfer as small a volume of BB:BA as possible. Too much and it won't set.