I do it pretty much the same as Mark does it. I added the NAV/GPS switch and usually import GPS Direct flight plans from FSX. Then the AP can track the FSX GPS flight plan. I usually file VFR plans at the outset and re-file IFR about 150 miles from the destination. Then I revert to Manual from VOR/LOC on the AP and follow ATC instructions to the Localizer. After recieving final vectors to the Localizer I switch from Manual to Auto GS on the AP. The AP then picks up the Localizer and also picks up and follows the Glide Slope right down to the runway threshold. I disconnect the AP about 100 feet from touch down. Works perfectly if you have the correct ILS frequency loaded in the NAV 1 radio. The only exception is there are some bugs in FSX at some airports where the ILS doesn't work properly. Not the fault of the AP!

Here's a link to a video where the AP works as I described above. At the beginning of the video you can see the 2D AP at the top. Doesn't really show the switches moving but trust me the AP is working as it should all the way to the runway. Don't get behind on the power as it is difficult to recover!!

http://www.vimeo.com/10510499

Bruce