Once you have bought your NMBS Standard Multi, you can easily use them when you pay for a NMBS ticket (from the routing or the Menu).
Indicate your from/to stations, and activate the toggle "Use a Standard Multi". The price of your ticket will then fall to zero. Click on "Pay to finalize your purchase.
You'll see a screen indicating that you can access your ticket from the homescreen of the app, and the number of your remaining tickets will be updated.