Okay, so please understand, if it is category destination that is the issue/concern, in the column: category_name_x, whatever you have there for each "instance" of the product is to which it will be tied.

If you want to have a product in main category Traditional Balls and sub-category Traditional Balinese Designs, then the category_name_x (sorry if I have the wrong field name at the moment) for the given product would need to be: Traditional Balls^Traditional Balinese Designs.

How you get there, that would/could depend on a number of things, but the important thing is that you can manipulate the data as much and however you would like to be able to end up with the store "arrangement" desired.

Basically, you have to assign/designate the category structure that you would like the/each product to have prior to uploading. Once uploaded, categories may get generated that are irrelevant or desired to be removed.

So, I'm not exactly sure (still?) what the confusion is or if it is just a matter that it takes "so much" to set it up the first time.

Ohh, yeah, so if you already have the product in the mega store where you want it and you don't want to add the product to any different categories, then simply delete the related category_name_x field(s) from the file being imported. That way, the product is not applied to any new category(ies) and is simply updated. Of course if taking data from the mega store to an individual store, want to be sure that the data fed to the "individual" store only applies to that store or at least is not carried over from something.