how do i make the game recognize the joystick when it is a usb one

In real DOS enviroment? You can't.

If you're talking about running the games in DosBox, USB joysticks or gamepads sometimes work and sometimes don't.

A somewhat reliable way to get them to work is using JoyToKey - vide this thread.

I have a wingmaster that can be programmed for .exe files so, that pushing a button acts as you would press "a" from keyboar for example. Now, programming it with explorer.exe makes it so, that the pad words in any game, even in windows. :D Very handy.