@louislanejr 

You will only be able to match the $3,000 deposit since that's what was deposited into your bank account.  The easiest way to do that:

1) Create a 'Cash on Hand' or 'Petty Cash' bank account in QB if you don't already have one.  

2) Receive the $4,000 payment on the invoice and deposit into the Cash on Hand bank account.  

3) Pay the $1,000 bill from the Cash on Hand bank account.

4) Transfer (New > Transfer) the remaining $3,000 from Cash on Hand to the bank account where the deposit was made.  You can match this transfer to you bank transactions.