It is actually done through the Item Class, not category.  If you have set up your items already, then you might have set up class codes since I believe it is a required field, but maybe not if you do not have the GL activated.
At any rate you will have to create item class codes, which can use default values (ones you set up for INV ASSET, COGS, Sales, and WIP as well as absorbed labor accounts when you set up the GL) or you can change any or all to do something different.  Then each item number needs to be assigned the correct class code.
If there are massive changes involved (lots of items, lots of class codes) you might want to go the Date Import route, which is explained very well on the evowiki site.