If the GCS version does not match the firmware version, then when you plug in USB the GCS will pop up a warning that says so. If you don't get this pop-up then they match correctly.
If you set it to "always armed", that is when you cannot save settings. It lets you save with "always disarmed". It's not good to use "always armed" for copters. If it won't let you arm normally, there is a safety reason why it won't let you arm and you need to figure it out.
If you are building a new quad, you might consider using LibrePilot 16.09. OpenPilot does not exist anymore. LibrePilot is effectively the next version of OpenPilot.
If you bought a ready to fly quad, then you should probably leave the version as it came until you find a reason to upgrade. There is a lot to learn to do an upgrade. A lot of work to avoid if there isn't a good reason to upgrade.