Yes, with trimmed surfaces, it is challenging to control where the edges will be located, when the surface is modified with control points.
It is best to create your surfaces so that they are within your boundary to start with and are untrimmed at least at the bottom edge. That is said, using the surfaces you have, here are a couple general suggestions of how you can modify to align:
Re-create the surface so that the bottom edge is NOT trimmed. This will help keep it in place when you edit the surface later. Attached an example. cobra final for rhino forum_RI.zip (6.9 MB)
Modify the surface, even if the bottom edge does not align. Now recreate the surface using Patch where you select the border and the “original bottom edge curve”. You might need to do a follow up editing, or adjust the patch parameters to get what you need.
I hope this helps.