Unfortunately, there is no relationship between shipping and payment in the settings. This has to be custom programmed.
You can check controller that process display for payment to add logic /storefront/controller/pages/checkout/payment.php
We are considering to add something that will help in this configuration.
Well,
No Manual Payment Methods Are There .I Will Explain This .Mostly All Shipping modules are ok .Take This Example .
Customer A Wants To place a order .He adds a item in his cart and selects "Local Pickup From Store " ,Then he moves to payment method there he is stuck cos he has one COD option and one cheque / moneyorder option .He wants to pay cash when he walks in the shop .Might Be a Module Called " Cash Payment " , One Module " Cash Deposit /Online Transfer To Bank " Or Just Called "Bank Wire Transfer " Is There .I Think If You can explain us or give us the code for the cheque / moneyorder module we can rename that as both these modules and use it .this is what i was explaining earlier too .Also i would like to ask can i add a module two times .For example i wanna use two diff courier systems can i add weight based shipping two time how .