Q.Can I disable certain payment methods with certain shipping methods?

Yes. To disable the use of certain payment methods with certain shipping methods, navigate in your Shop Manager to Operations → Payment methods, and click the (Edit) button for the payment method you wish to disable a shipping method with.

In the Available shipping methods section at the top, deselect the shipping methods you wish to disable. Click (Save) at the bottom of the page.

For example, in the above image, this payment method (COD) will be disabled when selecting Shipping Method B. This payment method will be hidden on step 3 of checkout when Shipping Method B is selected in step 2: