Yes and no! FS-UAE does not currently support multiple mice on the same computer (this may be supported in the future though). Another feature that is up-coming is using the analog stick an a gamepad to control a mouse.
But you can play it with FS-UAE today, but you then need to have two computers and use the net play feature. You can play over LAN, the traffic does not have to go over the Internet.
More information here: http://fengestad.no/fs-uae/launcher-net-play.