You should keep all related packages in the same project. The key question is what should be deployed together. If you need to deploy the parent and child packages together then there is no reason to separate them out into separate projects.
I would argue that if you need folders to organize all your packages then maybe your packages are too complex and intermingled. SSIS projects do not support virtual folders which is what would be needed here. Having said that though you could probably move your package files into subfolders in the file system and then add them using the "Existing Item" option to the project. It wouldn't change the layout in Solution Explorer though.