Thank you Dazz - it seems so simple but I completely overlooked Hyperlaunch. But once I edited the script correctly (and a few other odds and ends were tied up) it worked. Here's what I did:
- Downloaded AutoHotKey
- Opened hyperlaunch.ahk
Here I basically edited the MAME entry by changing the executable to MultiMame.exe at the head of the script and the "MAME" entry (and yes, I could have just changed the filename of MultiMame to mame.exe for simplicity, but I wanted to differentiate my different versions of Mame). Also, I had to edit
%rompath%%romname%%romextension% to just read
%romname%. I got that from something BadBoyBill posted on an unrelated thread in the Hyperspin forums and that fixed the problems I was having launching the game.
- Compiled the script.
- Created a mame.xml file through MultiMame and copied that to the database folder of Hyperspin's MAME section
Though, for some reason, it wasn't working the way I had intended. So instead of troubleshooting, I decided to simplify. I manually added the three Daphne files I wanted to combine with the Mame list to the default mame.xml file, making sure the file names matched the daphne.dat I used to setup MultiMame and also the theme names in the HS media folders.*
- Made "Dummy Roms" for the Daphne games to place in the main roms folder
- Changed the HyperSpin settings to launch games via HyperLaunch
And VIOLA, worked like a charm. I choose Donkey Kong from the list and it runs the .99 version. I choose Bubble Bobble and it runs on .116. Though I'm getting errors when I run the Daphne programs, it's definitely not HS related (my settings/folders are wrong as I moved things around).
I have a thread over at the HS Forums that I will add the above to as well. Thanks for the help Dazz!

(*BTW - The reason I needed to make sure the mame.xml database in HS matched with the theme names is because I set the options to THEMES ONLY as a way to pick and choose the games that are running on my cab and HS will not work if you have a theme who's name doesn't have an entry in the xml file.)