At present, the deployment process is not open for extension. We’ve got an internal feature request to allow the type of modificaitons you’d like, but it has not made it into the product yet. For MyEclipse to properly deploy your enterprise projects they really need to be laid out as expected, currently. If you ran your custom Ant tasks prior our deployment, would they then put the projects into the configuration our deployer expects? If so, although manual, this could work in the interim for you.
–Scott
MyEclipse Support