How is the courier charges paid to the logistics partner? Is this a automatic deduction that happens during Shipping transaction booking?

The courier charges have to be paid to StoreHippo directly incase you are using the available shipping partners in the StoreHippo backend. The shipping bill needs to be cleared periodically, and the bill is postpaid. However, in case you are using your shipping account, then you can pay them directly. There is no auto deduction, you can see all your shipping rates against each and every order in the shipping ledger and clear the dues from the back-end itself.