My advice would be to decompile an existing model similar to what you want to make and see how it was set up. I'm guessing there should be a bodygroup for the vest, but in case there isn't the custom vests that people make probably just overlay the default one (check this by decompiling).

For the scout arms, just assign the geometry to the respective bones and import it. If there isn't a specific spot to choose from, choose what best fits the model. The checkbox system is just for Valve.