The other way I could have done this was to use the manage sales tax and used the adjust sales tax window, however when I did this it didn't actually adjust the account it just put a new entry under the account. For example if it said we owed tax amount for state A for $100 and really it was $150. when I adjust the amount instead of adjusting it to STATE A $150, it left that as $100 and then put a separate line underneath with +50.00 which becomes quite messy.
QB has always done this, and doing so reflects the actual account entries. There was x-amount due and then the adjustment changes that. Just be sure to check off both the tax due line and the adjustment together before clicking pay tax.
How can I get rid of those adjustments from the record deposit window? Is there a better way to adjust these taxes?
An adjustment should never hit banking, the adjusting account should be set to an income account the adjustment is lowering tax due, or an expense account if the adjustment is increasing tax due.
What type account did you use on the adjustment?