<edit>modified to reflect correct software commands</edit>
Randy,
Is your software controllable by the 49-ways themselves? I may have just missed this in the thread.. Until there's more FE support, would be cool if (like in MAMEWAH) you could launch CPViewer to see the controls needed, then launch your app to select the appropriate joy. Not automatic, but easy 
*grumble, grumble* Now I have to buy more controls and encoders *grumble, grumble*

Thnx 
If
I read your question corectly, then maybe in at least five different ways -
If I understand what RandyT is doing and MameWah (which I don't use) -
Let's use PacMan as an example and assume that RandyT's software has a command-line mode with a command of
"GPWiz49.exe 4" to select 4-way mode.
Two ways to do it in software switching:
Method one - Create a batch file named pacman.bat with the following commmands:
C:\GPWIZ49\GPWiz49.exe 4
C:\MAME\mame.exe pacman
C:\GPWIZ49\GPWiz49.exe 3
Save this and modify MameWah to launch pacman.bat when you click on pacman in the gameslist. No need for CPViewer or frontend support with this method, but a pain to write 5,000 batch files.
Method two - Create a desktop shortcut named "4-Way Mode" with a target line of "C:\GPWIZ49\GPWiz49.exe 4"
Launch MameWah and CpViewer - Minimize to the desktop - click "4-way Mode" Icon, Restore Mamewah. Start Pacman.
One way using a rotary switch - Wire and label a rotary switch for each Mode. Launch Mamewah and CpViewer. Rotate Rotary Switch to 4-way position, launch PacMan.
Two methods using classic mode (Method two may not work - UPDATE - Will not work now that I think about how 49-ways are connected).
Method one - Let's assume that P1B3 with the Mode key selects 4-way mode (it might be a different button).
Launch MameWah and CPViewer. Press the Mode Button, and P1B3. Launch PacMan.
Method two - Assuming you literally meant using the sticks to select modes - limits you to 4 modes, say Raw 49, 8-way, 4-way, 2wayV. Let's again assume P1B3 selects 4-way mode. P1B1 selects Raw 49, P1B2 selects 8way, P1B4 selects 2wayV.
Wire your joystick so that UP activates P1B1, Left activates P1B2, Right activates P1B3, Down activates P1B4 (again no way to do this, I think I was thinking of the normal GPWiz at the time).
Launch Mamewah and CP Viewer - Hold the Mode button and move the joystick to the Right. Launch PacMan.
Sounded good if it would work.

Alternate idea - I'm not sure if the above was what you were asking or if you meant "Can I modify the graphic that CP Viewer generates so that when it says PacMan is a 4-way game, it also tells me to press the Mode button and P1B3 to select the mode?" This answer is "Yes, I'm sure you could, but I don't use CP Viewer enough to tell you how to."
Again, thanks to Randy for making such a versatile product (as usual).