I had this same confusion.  I am not a tax professional- just a thorough bookkeeper for my own small business. This is where I landed on this issue:  You're not double-booking the expense.  The expense is tracked through payroll and shows up on your income statement (P&L.)  These accounts were auto-generated when you signed up with Guideline (although both Guideline and QB seem confused as to who initiated that- but no matter.)  The debit that you see in your feed should be booked to the associated liability register.  Liability registers track debt or obligations and show up on your balance sheet- not your P&L.  So, when you book the debit from your checking account and apply it to the Guideline Liability register, you're simply tracking how much of the payroll expense you're remitting.  So, no double-booking.  One account is tracking the expense.  The other is tracking the liability (debt) associated with the program.