Okay, I finally got it to work and thought I'd report back as to what went sideways.
When I first set out to add a ringtone and realized that setting it to sync (or auto sync?) meant losing my other media, I set out to perform the sync manually.
I either got incomplete instructions or interpreted them wrong but I thought it said I could put a ringtone file on the my desktop and then drag/drop it directly to my iPhone. iTunes did seem to let me do this and even showed me a graphical representation of it happening. Once done, I had a grayed out "ghost copy" of my ringtone in the Tones folder on my iphone but it wouldn't show up as a ringtone in the phone settings. I tried to delete the ghost file but it wouldn't delete.
I subsequently found a set of instructions telling me I could perform the action as above but had to import the file into my Library and drag/drop from the Library NOT the Desktop. Unfortunately, having once done it wrong, nothing under our big yellow sun would work.
Finally, more out of frustration than anything else, I right-clicked the Tones folder (iPhone) and opened it in a new window. Once in a new window, I could delete the ghost file (wth?). Once th ghost file was gone, I drag/dropped the ringtone from the Tones folder in the iTunes Library to the Tones folder on the iPhone and everything works like it should.
I am still managing the media on the phone manually (meaning I drag/drop only the songs/playlists/media I want from my iTunes Library to the phone) and the ringtone behaves the same way.
I still think iTunes is broken and probably the weak link in the iOS offering. I should not have been able to do something so easily to disrupt functionality.
Anyway, thanks for all your input and creativity in helping me solve this problem. I realize it's a small thing to get snagged on and I appreciate your help. I think I learned a lot about how these two systems (iOS & iTunes) work.