How to deal with payments made on a company credit card?
So long as the credit card belongs to your business, not to you personally, set it up as a bank account, choosing the option "Credit Card Account" from the drop-down menu.
When you use the credit card for business transactions, you can either upload the transactions into FreeAgent and explain them if the credit card allows online access and downloads, or you can enter the credit card payments manually.
And when you pay off the credit card balance from your main account, explain that as a bank transfer.
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