Quick answer: go to Settings (gear icon) > Medicine Catalog, filter to YAKAP > Covered, and enter the actual unit price for each medicine.
Medicines are one of the components Tranche 2 is scored on. Medicines without a unit price may not be counted, which lowers the score your Tranche 2 payment is based on.
To be clear: this does not stop you submitting. You can complete visits and submit Tranche 1 and Tranche 2 without it. It affects how much of the medicine component you are credited for.
Use the filter, or you will be looking at the wrong list
The Medicine Catalog opens showing every medicine, which is more than 2,400 of them. Only a small share are YAKAP-covered.
Step 1: Open the YAKAP filter at the top right of the list.
Step 2: Choose Covered.
The list drops to just the covered medicines, and the count shows above the table so you know how many you are working through.
Tip: you can set a default Dosage, Frequency and Quantity per medicine on the same screen. Those auto-fill when you add the medicine to a prescription, so it is worth doing at the same time.
How medicines affect Tranche 2
Tranche 2 is a weighted score across consultation, laboratory and medicines rather than a flat amount per case. A component you never record scores zero and you lose its share.
See How is Tranche 2 computed? and How to submit Tranche 1 or Tranche 2 cases.