RandomDOSUser, your post is a little confusing. What exactly is it you want to do? Are your Joysticks detected by DOSBox? If they are, you should see something like "Using joystick XBCD XBox Gamepad with 6 axes and 24 buttons" in the DOSBox Status Window. If this isn't happening, you could try to remove one of the Joysticks, and retry.
Are you aware of the "Mapper" screen inside DOSBox? It can be accessed by pressing "CTRL-F1", and will allow the mapping of keys and Joystick controls. The maps can be saved, and loaded later to activate specific configurations (see the readme for details). With the mapper, it should be possible to handle all possible configurations. For example, i've mapped many of the keyboard commands of "TIE Fighter" and "Tomb Raider" to Joystick buttons, and it works like a charm. If you want to use more than 4 buttons on your Joystick, you have to set "buttonwrap=false" in dosbox.conf.
If you really want to use an external application for mapping, i'd suggest you try out Xpadder. I have recently found this application, and i think it's the best in it's field. It may look a little complicated at first, but it really isn't that hard to setup.