First define individual tax rates under Store Operations Manager, Database, Sales Taxes.
Then define the possible combinations under Database, Item Taxes such as one entry for Local and another for Local+State. Then select Wizards, Inventory Wizard, Task 170. Select departments or categories, display the worksheet, change the first entry to desired item tax, then use right-click to copy that entry and right-click again to paste to all rows. If satisfied with the results click Commit. Repeat steps for each group of items that requires a tax change.