Currently I have been working with the Beta versions and am getting the latest install now.
Working with 1011 simple items, 254 grouped items, 400 main/secondary/tertiary categories, the past install was slow.
It was also painful adding all the categories by hand.
I had to up the timing/memory for the upload process.
If you up the max_execution and also increase the memory allotted from 128 to ... 512+. You could probably push all 50,000 at once.
For me the upload process of 1011 items was about 3 minutes, and then had to run a script to update the storeview/website values with the item ids.
As of the previous version you would have to manually Pre-make all of the categories in Magento’s admin, then you can discover their category ID’s and then add those to the category_id next to every item on your import for products. If you do that, then it would show all of the items in the matching categories.
Through the Theming process and some remote calls to Navigation.php in the admin, you are able to create a vertical/layered/faceted navigation.
Hope this helps.