HCl has updated his Armada Online procedure to incorporate the improvements made in Origin's Armada Patch. In addition the joystick and internet functionality that he has included, the patched Armada adds passwords for each gauntlet level (in single player), more stability and darkening/lightening of the HUD crosshairs. You can download the new update here.
Detailed instructions on running Armada online are available here.
I've been getting more interested on the pre-Vision WC games lately, so I'll be revisiting a few ideas on my ever-growing "to do" list involving one of these games. This means that I will probably be halting Armada-related modding in the near future. I'll keep you up-to-date regarding any developments.
One final update being considered is adding the ability for both players in an Armada/Campaign battle to choose the Confed or Kilrathi faction at the same time.