If I understand correctly you want to have an Eclipse project in a sub directory of a larger repository. I think there is no reason for you to use "subrepositores", instead you can use the single monolithic repository.
- Using MercurialEclipse or another tool clone merc.myorg.com/hghome
- Create the sub directory myapp and in it create an file with the name ".project"
- In ".project" add appropriate Eclipse project configuration. For example
<projectDescription><name>myapp</name>[...]</projectDescription>
. - Commit ".project" and push it to the central server.
- Using MercurialEclipse clone merc.myorg.com/hghome again. This time on the last page it will allow you to import "myapp" as a project. It will show up in your workspace as an empty project.