Hi Arkie.., yes but within limits this gets a little messy, if I have understood your question correctly . . .
You can create custom categories for use within your eBay store but at present only eBay listing categories can be used in your Auctiva store.
So unfortunately you cannot use your custom eBay store categories in your Auctiva store and the category search option with keywords is difficult to set up efficiently.
However your custom store categories are available when creating a listing with Auctiva so the listing appears in the correct category within your eBay store.
If I have got this wrong then someone else will soon tell us
(Apologies if I am treading on your toes BroJames.)