Okay, I've copied a couple DVDs using
http://www.doom9.org/index.html?/mpg/maestro2.htm as a guide
I have all the chapters correct, the subtitles correct, and when I click on the video file that I've made from DVDMaestro it works correctly on my computer. But the menu never seems to work. There is an important part to the coping process is under the heading "How the hell do I get it all back together?? " in the guide. The way that I interpret this section is that I am to take all the files off of the original DVD except the VTS_02_1.VOB, VTS_02_2.VOB, etc (for the example that the guide uses). files which those I get from the DVDMaestro compilation that I created.
Then after that I wondered about the IFOUpdate section. I have all the options selected except for 4,5,7 (starting from the top of the options menu and counting down.) The mode is set at standard. Then for the original I set it as the VTS_02_0.IFO that I get from the DVD and the Authored I set it as the IFO that I created from DVDMaestro. Then I use the IFO that IFOUpdate gives me on the DVD I want to create.