Once I schedule a shipment, the payment of shipping will be made to the logistic partner on pickup?

If you use Shippo services, we'll be paying the charges on your behalf and would be reflecting the same charges to you. You can view the charges from your admin panel and make the payment from your admin itself. For more details, you can refer Shipping an order.

NOTE: Your admin will get blocked automatically if the charges go beyond Rs. 5000 (Credit Limit)