I would like to know how to set 2 different VAT rates under same agency and set the invoice form to show the taxable amount as per each rate and the tax amount per rate

I got your back, @samhonduras-hotm.

In QuickBooks Online (QBO), you have the ability to create tax rates. However, we still recommend consulting your tax or accounting advisors regarding the applicability of these rates. Let me guide you how:

1. Go to the Tax Centre by clicking the Taxes menu.
2. From there, select the Add Tax button.
3. Next, choose which type of tax rate you want to set up.
4. Input the details of your tax rate. You can also click the help button (yellow question mark) if you need help doing the process. 
5. Once done, click Save.

I've attached this article for your reference about the outlined steps above: How do I set up sales GST/VAT rates and use them on forms? (International QBO). 

Also, in QBO, it's easy to record, adjust and delete sales tax payments in the sales tax centre. For the detailed instructions, check out this link: Manage sales tax payments in QuickBooks Online.

I'm always around if you need additional assistance in adding tax rates in QBO. Don't hesitate to post a reply below. Take care.