Once your project hierarchy is created, you can start assigning effort estimates. Since superprojects (projects that contain subprojects) are merely placeholders for the collection of their subprojects, effort estimates are assigned only to task (bottom level projects, that contain no subprojects). The effort estimates of superprojects is just the sum of the effort estimates of their subprojects.
If you have broken up the projects in your hierarchy till the right level, it will be easy for you to estimate the effort each task will take. You can enter this value into the Estimated Effort column for that task by double-clicking the cell.