What if you want to display an additional charge in the estimate and invoice that is based on a percentage of the estimate (invoice) total to cover the cost of accepting payment by credit card? ContractorTools does not have a specific way to handle this, but there is a way to do it in reverse. Here's how:
Increase the total percent of your markups by the credit card charge amount (i.e. 3%).
Add a discount of 3% (Job > Job Info > Discount) to the job for "Cash Discount".
Add a note in the job terms (Job > Estimate > Info > Terms) to the effect that "The total price will be discounted by 3% if payment is made by check or cash."
If the customer pays by Cash/Check, include the discount; it will be displayed in the estimate and invoice. If they pay by credit card, remove the discount.
You can set up the discount and terms in your job template(s) so you don't have to do it repeatedly in each job.