Taxes and fees can be broken down by each Ticket Type which will determine what Ticket Type will be responsible for the taxes. This will take set up before you start invoicing tickets. You can do this by going to this article Configure Ticket Types (New) | Articles | Omnique Shop Management | Intercom.

You can set up Ticket Types to have a default Payment Type and if you want it to have taxes you would want to have the "Is Taxable?" toggled on.

Once you have the Ticket Types set up, within the Ticket Info on the RO you can choose the Ticket Type.
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In this scenario the customer will be responsible for the part so the Ticket Type will be set as Customer Pay and the labor will be for free under Goodwill. Doing this will make the customer responsible for the taxes, which is why the Ticket Type was set to Customer Pay.

This is what the invoice page will look like.