ContractorTools does "job based" accounting, which means transactions (invoices, credits, and payments) are not applied to each other, but are automatically applied to the job balance. As such, ContractorTools does have not a way to apply payments to invoices. This means that when you sync with QuickBooks, payments are not applied to invoices in QuickBooks.
Please click on this link for information on the correct procedure for managing payments entered in ContractorTools.
ContractorTools does not have the ability to apply payments to invoices because it can get quite complicated when there are multiple invoices, and payments with amounts that don't match the invoices. Based on the questions we're getting about this though, we will eventually make it so that ContractorTools will automatically apply the payment to the invoice in QuickBooks if the amounts are the same.