Bemeister Knowledge is the key

Alfresco 3 comes with a more transparent amp feature. In fact the MMT tool is still used, but there is an amps directory available and an apply_amps.bat (apply_amps.sh on linux).
And then it's easy. Just place your amp files in the amps directory and run the bat or sh file.
However: If it worked properly, I did not have to write this. It seams that the most important rule in the file does not work out-of-the-box. And that's because there is a "%2" at the end with no meaning. So you should edit the bat file and remove the "%2" after -directory in the mmt install line.
The sh file for linux works well from the first time.
Another important option of the MMT tool is -force. When testing amps, this forces the amp to install even if exactly the same version is already installed.
But, when you want to develop AMPs, I can only advise maven: http://wiki.alfresco.com/wiki/Managing_Alfresco_Lifecyle_with_Maven
There are also flaws in the POM generated by the sourcesense archetype, but hey. After a bit of investigation you can get the integration-test phase to work using the webapp profile. And then magically Jetty will be running alfresco including your amp. Hereby the pom that does the trick.