Here is a pic of the config page for flashcut 2. Its really easy to have different settings for each axis/ballscrew. You can also save different configurations as a setup file, and run different machines with just a quick reload of the setup file.
(disregard the numbers in the boxes, this isn't a working config)
Here is a pic of the screw setup page:
Here is a pic of the Jog/control screen:
You can use [ctrl]-[arrow key] to jog, so adding a pendant or hacked up keyboard would be no problem.