I can't picture exactly what you're describing, but I think the bottom line is that there's a difference between the TOC, which is displayed in the final output, and whatever arrangement the topics have in the Project Manager pod. I'm guessing you're using RH8 because any other version automatically displays items in the Project Manager in alphabetical order, and they can't be rearranged except to be placed in folders.
If you're concerned more about how your topics are listed in the Project Manager, I believe RH8 allows you to drag the topics into any order you want them to be in. (I use RH7, so I'm going from memory.) However, this doesn't affect the TOC unless you auto-generate a TOC from the arrangement in Project Manager. To work on your TOC, expand the Table of Contents item in Project Manager, and then double-click the TOC there. You would need to add new topics manually to the TOC.
I don't think there's an automatic way to create either topic folders in Project Manager or in the TOC—so you manually create them and drag and drop topics into them.
Hope this helps answer your question.
For folders, I'm afraid that you will need to manually create them if that's what you want. No way past that as near as I can tell.
If you are using RoboHelp 8, Adobe added a new feature that allows you to present the Project Manager pod in any arrangement of topics you want. Basically you may drag them around. I'm thinking it may also list them as they come in. So that may help.
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No worries Rick, when I turn sideways I'm invisible.