There are currently two options within the Execute Package Task to execute child packages: Project Reference and External Reference. The problem with project reference is, that all packages need to be within the same project folder. This makes it hard to organize many packages for a large project.
If switch to External Reference combined with SQL Server, I can not see the SSIS packages which are deployed in the new SSIS db, when I choose the SSIS DB as source.
So Project Reference seems to be the only option for deploying packages to SQL Server. To use Project Reference, it has to use Project Deployment Mode, which doesn't support SSIS configuration! It has to use project parameters to store variable values and use parameter binding to pass parameters to child packages.
Denali really sucks!