Reorganize a Magento Database & Import API

Project Description:
I have a magento website and a working script that imports all my products and categories from my supplier. It also sends my orders back direclty by API.

What i need from you:

Though the script works, we need to map the categories and tweak a few minor things for the product display. We also need to set up some top level categories that the sub-categories and products will slot in to.

For an experienced programmer this should not be hard as the code is all written, we just need to organize it on my site.

I will provide full documentation with instructions.