ctlModuleMaker child items and pagination

[edented]

Hi,
I have a module with 3 mainCategories, 7 subCategories, and 40 final items.

Usually i call for the items directly by their subcategory and all works well.  However, if i try to call for the items belonging to a main category, (eg- encompassing 2 subcategories) the results show all of the final items. 
For the pagination, the total number is 280 (finalitems x subcategories).

How should i call the items belonging to a mainCategory so that it reflects only its children?
Is there an easy place to change code to figure the pagination?

thanks