I was asked by Support to send in these suggestions:
"I was very excited to see the new QBO integration but there are several issues with the options for setting it up.
  1. If you choose a Sales Receipt (by transaction) then it creates a Sales Receipt that deducts the fee right on the same transaction. The result is that a donation does not show as the full donation in the donor record in QuickBooks.
  2. There is nowhere to choose a Class allocation for the transactions. Most nonprofits and many churches require a Class to be allocated to each transaction for tracking of the 3 functional categories for the IRS. (Program, Admin & Fundraising)
  3. This is small but when choosing the QuickBooks account for mapping of individual funds, your drop down box shows all inactive/deleted accounts as well as active accounts.
It seems that the option to have a deposit transferred instead of a Sales Receipt may be helpful for some organizations.