Shopify payments - Adding extra charges

I just switched to Shopfiy Payments from Bambora in order to avoid the transaction fees. With Bambora I could log into their system and add a charge for shipping if they emailed and said they wanted to change to a different more costly shipping method or if they made changes to their order. Is this not an option with Shopify payments? Do I always need to send it as a separate invoice and have them log in and pay for shipping separately?