hi kk,
here's what worked for me roughly following the help for hcp here.
1) I created a sub-package in my hcp package similar to what you did
2) I then created a new xs project but did not share it right away with the hcp's sap repository, only saved it locally.
3) after saving the project locally I went to Team > Share, selected my hcp system and then pressed the Browse button and navigated to my sub-package from step 1
4) after pressing OK and then Finish
I was able to successfully add a new project into a sub-package. adding new files and activating the project was also successful.
I hope this helps,
jamie