If I use a more shallow container, is it ok to move the clamp down so it is positioned on the metal tube? I didn't know if it needs to always be at the top of unit (resting in the plastic area at the top.
Yep - I normally use gravity or the bottom of the pot to hold my APC in place (I don't tighten the part of the clamp that would keep the APC from moving). The skirt is a cylinder, so anywhere along its length is going to keep the APC in place.
You can watch the video from Anova as to how to use your APC: