On Windows XP, Dosbox has its .conf file in the same folder as the executable and everything else. This means one could copy the files from the Dosbox folder into another folder and modify the .conf folder there to do different things. Run one Dosbox executable, it runs one set of instructions. Run the other, it runs a different set of instructions.

I used this in such a way that the necessity of typing in:
MOUNT C GAMES
C:
CD DAGGER
FALL.EXE Z.CFG
at the startup was negated to the click of a button.

However, now that I've upgraded to Windows 7, Dosbox now only refers to one .conf file in its own folder in the Appdata directory, which means I can't make use of different .conf files.

Maybe this would be more appropriate for the Dosbox forum, but is there any way to do the thing I did on Windows XP in Windows 7?

If dosbox is anything on windows like it is on Linux, then you could give it the name of your conf file on the command line: dosbox -conf myfile.conf
Maybe you could drop that command in a .bat file.