Sorry if I have missed this information, we use Shopify Payments for the website orders but I am unclear on the fees or percentage of sale that Shopify would charge for orders on eBay or Amazon that are imported via an app. The orders are paid for on the respective channel and not on Shopify but are brought into the Shopify Dashboard.
I don’t think there’s a fee for importing orders, but you could check your order timeline to be sure.
On regular orders you’ll see something like “Shopify added $xxx to your next payout”, that amount is less than the order total if used Shopify payments.
Shopify Payments will not take any fees for orders imported via the API (via an app or channel.) Your eBay and/or Amazon orders will be imported for fulfillment purposes only. You will not have any transactional details/info since the payment is external.