Do you mean just using the keys mapped with joytokey in mala only? I have tried this but I have had trouble getting joytokey to shutdown and open again with mame. If it is running and you hit a keypress, it should not cause any problems as long as the key is not mapped to anything extra in mame. Say your joybutton1 is mapped to B. In mame if you map this key to player 1 button 1, it will show up as joybutton1-B. This causes no problems and you could always manually shutdown joytokey, do the universal mame map, and then reopen mame. The keypresses sent by joytokey will have no affect on mame whatsoever.
I had to do this with mine so that I could emulate 4 or 5 buttons on some emulators for keys like Exit=esc. I just shutdown joytokey and did my mapping in mame. Everything works fine. Just double check the buttons you use for joytokey are not mapped to anything extra in mame like frameskip or screenshot.
On another note, to get joytokey to load on windows start, I added it to the startup folder. You will notice that when this happens it does not start your mame config file but the default one in My Documents. All I did was modify this one with the inputs I needed for my cab so it will load it on system startup. There might be other ways to get this to work, but this was the fastest and least problematic method I came up with.