Hi Scott,
Please note that when you compute use tax, payment of that that is your responsibility, not the vendor's responsibility. Therefore, the tax should be going to a separate tax liability account not to vendor account. You may either debit the material / fixed asset account or tax account in GL.
Under Transaction Key (Environment > Transaction Key), set Posting indicator 2 separate line item so that you can see them in line item report.
The tax amount should be posted to a liability account by month end processing, and by using separate tax returns, you can remit them to the respective state tax authorities. In most states you can submit them electronically as well.
Regards,
Unnivel