Hello soyeso,
Do you mean that the MIDI ports from your MOTU Microlite aren't listed on Hauptwerk's 'General settings | MIDI ports' screen?
Hauptwerk just queries that list of MIDI ports from the operating system at the point in time that Hauptwerk launches. (It doesn't support 'hot-plugging' audio/MIDI devices, so you need to make sure the MIDI interface is connected and powered before you launch Hauptwerk.)
Have you downloaded and installed the current driver for the Microlite? If not, it can be found on MOTU's website here:
http://motu.com/download
(It's the 'MOTU MIDI installer'.)
After installing, reboot the computer, make sure that the Microlite is attached to the computer and that its green ('Computer I/O') LED is lit, before you launch Hauptwerk.