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You've discovered one of the drawbacks of converting projects to action groups! It is showing you all the projects, but you don't have as many of them as you did before the reorganization. You also can't review them separately, put them on hold, etc.

If you want the smaller "projects" to retain the flexibility and visibility they had as full-fledged projects, I would suggest organizing with folders as the major containers. The disadvantage here is that it is more cumbersome to indicate that this project must not start until that one finishes, etc. Of course, nothing prevents you from having a folder with a couple of big highly structured projects and some smaller ones on the side that don't need to be closely synchronized.

To extract a nested project, just select the part you want to take out and outdent it until it becomes a project. Cmd-[ should outdent one level.