Do you need only accessible using mydomain.net/MyApp
or show the url to users while accessing?
A simple way is to use a seamless iframe:
1. Create a dir in FileMaker Server/HTTPServer/conf called MyApp. If mydomain.net points to the filemaker server mydomain.net/MyApp will be serverd for you there.
2. Create a file index.html in that directory
3. Use code something like this:
Caveat is that you can only do this on the same domain&ip. So you can't iframe from a site on mydomain.net to myfilemakerserver.net for instance.