Once you expand the Transaction tabs, you will see the Custom tab. This is where you will enter data specific to your Brokerages requirements such as PID/Roll Number, Registration date, etc. to populate reports such as the Other Trade Record Sheet (Other) or Conveyancer Instruction report. This data will also populate the Conveyance Letters to Buyer Broker, Listing Broker and Sellers Attorney.
The MLS Fee Invoice Received Date relates to the Enable Discounts panel of the MLS/Transaction Fee.
Expanding the User Defined Fields panel will allow you to enter data reported on the Transactions by User Defined report via Reports / Transaction Reports.