How to patch a hole in the shell. I want to offset a shell from a ball

Just like you would cut a hole in a part. Create a sketch, cut though all.

As for the shell  question, you can use a surface fill to patch the hole in the shell.

In Assembly Features, you can make a cut very similar to making a cut in a part, and you will have the option of having the cut apply only in the assembly, or have it edit the part files.

For patching holes I am a big fan of the "Delete Face and Patch" tool. If you are talking about surface bodies, I use either "Delete Hole" or Untrim.