The use tax is in lieu of the sales tax. If you paid use tax, then sales tax doesn't apply. If you paid sales tax, then use tax doesn't apply. Check the tax laws. Sales tax covers transactions made wholly within the state. Use tax covers when sales tax doesn't apply. They are usually at the same rate, or some set rate, depending on the state (Sales/Use tax may be called something else depending on the state - in New Mexico it's gross receipts tax for within state transactions and compensating tax for out-of state transactions shipped to NM).
If you paid one, then you don't owe the other, if you paid neither, then the state can come after you for the taxes due. Use tax is not a violation of the commerce clause. States may tax items within their jurisdiction, and the use tax would apply as the item "came to rest" in your jurisdiction. The only time it would be a violation is if the states the product traveled through tried to collect taxes on that item. That'd be like Nevada trying to tax an item that someone in Utah bought from California. That won't fly, but Utah taxing the item is lawful. I'd rather pay use/sales taxes on goods than income tax. What sucks is for the on-line retailers to have to track more than just 50 rates. Some states have one rate than rarely changes (like Idaho - at 6%), some have multiple jurisdictions (in NM, just about every city has its own rate, which changes in January and July every year) and often these rates change throughout the year.
Thankfully, NM taxes out of state items at a fixed rate, regardless of where you live. I live in Rio Rancho, Sandoval County and my sales tax rate is 7.4375% for the last half of this year. But if I buy something from out of state, the rate is only 5.125%.
It's the same technique as calling tax deductions, "tax expenditures" or what's in that abortion of a debt ceiling deal "cuts."