I have the regex for finding my alts figured out, but I'm not sure what to do with the regex for the main, so I thought I would ask. I have it set right now so that if there is no result, it gets set as a main. I would rather make it set them as a mainless alt if there is no result, so I can see who needs their notes changed/updated.

Examples of my player notes:
Main | Ench/Ham-Smith
Alt of Krellen | Eng/Skin

Regex:
/^Alt\sof\s(\w+)/i *works*
Main *doesn't work*

The main identifier is not a regex but simply a string. With your setup the main identifier would make someone main if his note was "Alt of Main".
The correct configuration is turning the defmain setting on (it is by default I think) then any character for which the regex doesn't match anything is a main.

If that doesn't help I need a site url and a piece of your 'update relations' log

Site:
http://www.infernalprogeny.com/roster/
Update Log:
http://www.infernalprogeny.com/main-alt_update.log

As I said above, I do have the "defmain setting" on:
Regex | /^Alt\sof\s(\w+)/i
Apply on field | >Public note<
Use match no | 1
Main identifier | Main
No result | [x] Main - [ ] Mainless Alt
Invalid result | [ ] Main - [x] Mainless Alt
Alt of Alt | >Set as mainless alt<

Maybe you don't have it configured to do what I had imagined it would do. I guess I could look at your code and see, but I'm lazy. Anyway, I want it to also search through player notes for the "Main identifier." The way I have it setup in my in-game roster is like how I tried to say above. If the character is an alt, their player note says "Alt of MAINCHARACTERNAME." If the character is a main character (regardless of if they have alts or not), their player note will start with "Main." Yes, just the word "Main."

Now, if there is "No result" for whether the character is an alt or a main (in example, someone with a blank player note), I want to turn the "defmain setting" off so that they are considered a mainless alt. Right now when you hover over someone in the Main/Alt roster page it says almost everyone is an alt of themselves (Babyt: "Alt of Babyt"), but if someone really does have alts, their main is indeed considered a "Main." Hmm...

I hope I explained my situation a bit better this time.

What you describe is not possible currently, but it's a nice idea. I might implement it at some point.

The tooltips have a logic error. I'll fix them for my next release.

I got hit by an inspiration. Try this alt regex:

/^(Main)|^Alt\sof\s(\w+)/i

And set the main identifier to Main.