One may add invoice items into 3D that calculate based on a percentage (for discounts or surcharges, etc.), though the 3D program is not intended to replace actual accounting software.

Although you will likely find that using other accounting software for your invoicing is more convenient, you may add a new invoice item into 3D using Office management Customize>Invoice Items.
Tap Add New button.
Assign a brief name for the item, e.g. tax or discount.
Enter a longer description such as the type of tax or discount.
Set as a commonly used invoice item if you want it to appear at the top of the invoice item list with other commonly used invoice items.

Enter the percentage in the price field (e.g. 6.5 for 6.5% tax) and tick the box Calculate Based on Percentage.  A discount type item may be entered as a negative percentage amount.

Tap Ok to save the new invoice item.

Now when you fill out the invoice tab for a new job you may add your regular invoice items and the tax item to calculate itself based on the total.  See  program help topic for more details.

Note that if there are multiple taxes and one should be based on a prior amount that already includes another tax, you'd want to add all items except the final tax and then add it last after the other items were selected and calculated, due to the way the calculation process works.

Or if multiple taxes are supposed to use the same base amount, you could combine both tax percentages into one invoice item and indicate the respective rates in the description.  That wouldn't show the breakdown of the actual amounts though for each item, although one may manually adjust a number for an invoice item as well.

Verify your process to make sure the steps you use will calculate as desired, and then you should be able to use those same steps each time for other jobs.