First of all, commanders are key to ground combat as the bonuses they give are huge.
The bonuses do not currently pass on in the hierarchies.
Some testing I have done reveals the following about both HQ and ground combat command:
They only need to cover the formation they are in, not the formation and it's children.
To make a Hierarchy an HQ only needs to be larger so if your army is a standard size per formation you can just make the HQ's 2000, 2001, 2002 to make them work together as support hierarchy.
That being said, it seems larger formations do better in combat so using the element transfer to put all your ground forces into 3 formations (1 for rear, 1 for support, 1 for front line) and having HQ's and leaders appropriate sized for them would be ideal, if your front line is larger than your support you would be force to split it up into multiple formations as needed in order to keep the HQ bonus which again is key to winning combat. Splitting up formations into a bunch of tiny ones seems to be a micro-management hell that does not offer much on benefits.