I contacted Craig direct via email and he got back to me:
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I have never actually looked at the WHMCS code, but basically all you need to do is find the view where the 2Checkout HTML form is displayed and add this line below the form.
<script
src="https://www.2checkout.com/static/checkout/javascript/direct.min.js"></script>
This script will automatically hook into the form on page load and bring up the iframe when the form is submitted.
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I had a look at adding this to the 2checkout module however consider it is all in IonCube, I gave up.
Anyone have any other ideas?
Cheers.