Currently, the custom costs can only be set up as flat amounts. The ability to set them up as a % of other Costs or Sales in Lifetimely should help.
This is a solid need. We have a 4% cost of every order going to an operational partner that we can't account for in Lifetimely.
Workaround for anyone reading: I'm going to add the percentage to the Shopify payment processing fee, so 6.6% instead of 2.6%.