Thank you very much for the support.
By copying the .xmi files that Indigo generated and putting them in the MyEclipse project's WEB_INF folder I'm now able to deploy an EAR that shows up regularly on the WS console.
I have now problems when I start the server, though. The problem seems to be in the fact that we set up our project using Maven, and we make extensive use of Maven profiles and filters to fill in some configuration properties depending on the target server we want to deploy the ear to (for example: link URLs, homepage titles, logos, etc.)
When MyEclipse compiles and deploys on the WS in my development machine, cah I specify a MAven profile (or some equivalent action) in order to solve this problem?