Re: subdirectories
Toke, if you mean sub-categories you can choose the parent category for your sub_category by choosing "Parent" during the category creation. Parent would be your 1st level category, or any level for that matter, as tiki allows you to create sub-categories infinite deep. Please see screen shot:
Click on the "Parent" drop down menu and choose your top category you'd like your sub-category to be under. Hope I understood your question and this is what you needed.