Updating Existing Invoices
You can easily change who pays transaction fees for an invoice by going to the bottom section of your invoice and updating the dropdown that says "The client [will/will not] pay the processing fees..."
Updating Defaults For All New Invoices
You can change it by going to your "settings", "payment & invoices".
Note: clients paying transaction fees are only available when the client pays via Stripe (credit card or ACH) or PayPal.