Why are all of my free heroes not available in hero management?

If by hero management you mean the management station then this will only display development heroes that can help with the production of resources or training. You will also only be able to station heroes up to the amount of 'cost capacity' that you have which depends on the level of the management station building.

Combat heroes are only available to place in APC's by tapping on your Barracks -> Formation or tapping the APC icon which is the brown truck icon in the upper left of the screen.