I have run into two problems trying to do this from Setup Options > Path and URL Settings

1. This is really quite trivial. Maybe I did things in the wrong sequence, or maybe it is a programming oversight. When I changed the values of admin_root_url and admin_root_path (within cgi-bin) the new values were not written into all the public cgi files at the line beginning "use lib ...". Easily fixed manually.

2. I want to move all admin files and directories that are not cgi out of the public_html into the non-public file system. There are eight cgi files that should remain in the cgi-bin (including mysqlman.cgi), but I don't want anything else there. But Setup Options > Setup Options apparently does not give me that option. I haven't tried it yet, because I don't want to risk messing up all the work I have done so far, so here is the question:
"Can I move all the non-cgi files, then modify admin_root_path accordingly (so that admin_root_url and admin_root_path would be two different directories), and expect Links SQL to work?"

Overall, I need the files organized like this ...
Public cgi files: .../public_html/cgi-bin/links
Admin cgi files: .../public_html/cgi-bin/private
All other admin files: /usr/home/my_account/links_sql