Gydion: It's a common issue with multiple devices. Report back when you get a chance to try it.
Yes, DOSBOX is a bit clunky when it comes to multiple pad/joystick connected, especially if you want to use one for some games and a different one for others.
You can work around that a bit with the integrated mapping tool (CTRL+F1) or some external tools like JoyToKey, as suggested... speaking of WC1 in particular, i highly recommend this in any case, since i've always found the native joystick controls a bit odd (like the "double pushing" a button and stuff)