I just wanted to give a recommendation for folks using QuickBooks with WHMCS. I also use Stripe and PayPal for payments.
I purchased the Quick Books Online module from ModulesGarden which has been great to get customers, invoices, and payments in to QBO. My heartburn was I didn't have an easy way to deal with the transaction fees charged by the payment processors.
I found a service called PayTraQer that integrates Stripe, Paypal, and Square payments into QBO. They have a lot of options to customize how their service works for you. Initially, it didn't because the ModulesGarden module was already recording the payment in to QBO. PayTraQer was also recording a Sales Receipt in addition to the Fees transactions. After talking with their support they agreed I had a valid use case and added a feature to only record the fees transactions for me. This will save me so much time!
If you are suffering with the same problem I was having I'd encourage you to check them out. Their service is dependable and their support is super responsive via live chat.
https://www.saasant.com/app-pay-traqer-sync-paypal-square-stripe-quickbooks.html
Now I just need to find a solution to my weird tax requirements on some of my products to completely automate things. 🙂