Processing payments thru Acuity doesn't separate taxes. Can QB change the invoice after it processes thru Acuity? It seems like I cant change it after the fact.

Welcome to the Community space, @tara12.

Once you integrate QBO with Acuity, payments that are made will be automatically added as an invoice in QBO. Editing this in QuickBooks Online is currently unavailable.

I'd suggest reaching out to Acuity Support so they can assist you with the process using their tools.

Also, Acuity creates invoices in QBO without taxes. For US accounts, the taxes must be set up first in QBO. Once done, you'll have to check the Tax box for the appointment line-item in an invoice. 

If you have any other questions, let me know in the comment section. I’m here to keep helping. Wishing you continued success!