Hi!
Yes 2 tables would be the best, 1 for main categories and 1 for sub categories.
You should be able to have them in a singel php-page, both add/Edit/delete/move(edit)
As for Menu Writer, did you get the main category to show? And failed showing the sub categories?
I will try make a small sample and put it up when i get back home later today, se if that helps you out.
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Update!!
Here is the sample!
/Morgan