Hi Stacey,
From experience, many administrators have an expectation that once you upgrade a full support pack, all the notes should automatically be applied and no manual intervention is required.
However, as you have right fully pointed out, some notes (more recently compared to previous GRC incarnations) do indeed require manual implementation, but worth pointing out there are not that many. I have also found that some manual implementations are also dependant on which NW version the GRC system is based on.
My advice would be to perform a base functionality test on GRC AC once any pack is implemented and then where an issue is identified, identify the manual fix (or even a new note!) to resolve the issue.
As of late, I know a few guys have been just implementing SAP notes individually as per requirement, as opposed to regular SAP Support Pack updates as a safety measure, i.e. they do not want to introduce new bugs into a stable operating GRC tool.
I am sure everyone comes up with a sensible and suitable maintenance strategy that suits their company's needs.