From the OMS click Settings / Edit Compatible Software / Payment Gateways/ Preferences. Select 'Order Total plus X percentage'. This will authorize the order total plus a percentage. (We recommend reading the Authorization Amount Tool Tip thoroughly before making this change.)
Please note that to capture this amount in addition to the order total, you will not be able to batch process and you will need to take an extra processing step on each order:
When processing fee captures for orders, you will not be able to batch process or simply click on the $ tag icon on the order list page in your OMS. Instead, on a per order basis, you will need to click through to the Credit Card Terminal from the order summary page (blue button at the bottom) and click Prior Auth Capture.
This will open a window that will reflect the default to charging the order total. You must change that selection to 'Other Amount' and enter the amount you wish to capture (the authorized amount, if the order hasn't changed).
For orders that were in the system before you updated your authorization amount, you may need to void the initial authorization and auth/capture for the increased amount, because you won't be able to capture more than the authorized amount.
If these restrictions won't work for your business, consider adding a percentage or fixed amount to your shipping cost instead. Although this will apply to all orders regardless of whether a credit card is used, it may be the more palatable option for some merchants. To add a percentage or fixed amount to your shipping costs, navigate in your OMS to Settings / Compatible Software / Online Shipping Tools / Preferences. Or, consider a shipping override in Settings / Shipping / Shipping Overrides if it applies to your setup.