Currently, it makes the most sense usually to place the support elements (artillery, construction, supply, etc.) into higher-level HQs because of the way leader promotions work - ground force commanders always promote in a 3:1 ratio between lower and higher ranks, so you don't want to "waste" low-rank leaders on support formations which could be higher-rank instead.
In v2.0 officer promotions will be on-demand so you can do whatever you want. In this case you might have the artillery for example as low-rank formations alongside the line formations, and a "flatter" HQ structure with only a few ranks and the HQ formation has other support elements (logistics, etc.).
And how does replacing destroyed units work?
You can rebuild manually or use the Unit Series and Replacements feature from 1.12 onwards.
