Thank you for your interest.
To do so, follow 3 steps:
1. Make sure all your products visibility is set to "Catalog, Search"
2. Assign configurable products to the main category
3. Assign simple products to the sub category.
It can be done with Store Manager for Magento in 2 clicks (with no fee). Check free trial version at http://www.mag-manager.com/free-download
Feel free to contact us if you have more questions