Okay, I think I understand the problem here.
For example, if my first main category was Beach Games and inside that I had Beach Balls, and then I had a second main category of Sporting Goods and I wanted another sub-category in that called Beach Balls as well. Would there be a need to manually populate both categories.
I think you can get around the problem with Dynamic Categories and Product Types. In my example above, I would create a Product Type called Beach Balls and tag all my products intended for that category with the Beach Balls Product Type from the drop-down menu in the product main screen. Then I can set up my category structure but make the two Beach Balls sub-categories Dynamic rather than Static. Make the dynamic criteria based around the Product Type "Beach Balls" and run the import, and then you should be done. Any new additions to these categories requires the inclusion of the Product Type and then a Dynamic Category "Regenerate" but that will save you loading multiple sub-categories with the same types of item.
Either that, or I've misunderstood the problem. 