Hello,
About 1) for your upstream boundary, you could impose both -- use Thompson boundaries -- although it would be better if you multiply your h by you u,v, integrate over your upstream cross section to make this a bi-directional Q (+ entrance, -exit). The let TELEMAC do the rest (use velocity profile 4 for that boundary).
About 2) for your downstream boundary, you can still set the level even if is it dry. It will create a warning. Just make sure that the level set is not less than your BOTTOM variable (ZF). I would also use velocity profile 4 for that boundary as well.
Hope this helps,
Sébastien.