On Cura version 2.1.3, I simply swaped the shipped firmware with the firmware i wanted to get flashed.
In my case, i'm using OSX and the Cura app comes with a directory containing the firmwares:
/Applications/Cura.app/Contents/Resources/cura/resources/firmware/
I wanted the latest tinker firmware fetched here.
Simply replaced my version of the firmware for my machine:
Make a bakup of the shipped firmware: $ mv /Applications/Cura.app/Contents/Resources/cura/resources/firmware/MarlinUltimaker2plus.hex /Applications/Cura.app/Contents/Resources/cura/resources/firmware/MarlinUltimaker2plus.hex.backup
Copy our new firmware to replace the shipped firmware: $ cp -v ~/Downloads/Tinker-MarlinUltimaker2plus-*.hex /Applications/Cura.app/Contents/Resources/cura/resources/firmware/MarlinUltimaker2plus.hex
Update the machine using Cura: Cura > Extentions > Firmware > Update Firmware