Can't find any info on this, can anyone help?

Me too. I have been trying to control my copy with a Playstation Pad via an interface bought from Game - which every other programme I have tried to use it with recognises it as a standard joystick. The Alien Breed config programme doesn't even recognise a joystick is plugged in.

Can anyone give advice on getting joysticks recognised by this?

Personally, I've never had any luck getting a gamepad to work natively with any DOSBox settings. You can always use a program like Xpadder or Logitech Profiler (not sure if it works with non-Logitech controllers, but I don't think it'd hurt to try) and map the keyboard keys to the controller.