I don't know about MyEclipse, but the integration between WTP and Maven is horrible. Then again, I don't have a very high opinion of WTP as a replacement for sysdeo either.
If MyEclipse is anything like WTP, however, it doesn't adhere to Maven's standard project structure by default. Which means that if you create a project in Eclipse, you have to manually gimmick it up to be Maven-friendly.
Going the other direction (like you are) is even worse. There's a LOT of work that needs to be done in Eclipse as far as making it capable of detecting and applying external architectural considerations, even ones as simple as converting a generic project into a
Java project. Often the simplest approach is to create a new, empty project containing the facets/attributes you want and shovel stuff in from your
real project. Which can be especially problematical if the original project is already under version control and what you're trying to do is update the VCS project with the Eclipse-friendly one.
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.