I'm obviously doing something wrong, as I'm double counting many expenses and bills.

When I receive a bill from a vendor, I enter that bill as an expense in QBs.  I then 'make the payment' on that bill and print/mail the check to the vendor.  (the first expense transaction listed in QBs).

Once the vendor deposits/cashes the check (ie. clears my bank) and that transaction is accepted and added to my register.  (the second transaction listed in QBs).

All of my QBs transactions that had checks input and printed from QBs have resulted in double counting of expenses, and is negatively affecting my P&Ls. 

What is the best way to fix the problem(s) that have already occurred, and the best way to prevent them again going forward?

Please help!