Note
In the Overview, I explain my thinking. This is a fairly long article, but contains a lot of useful background information if you want to understand how I arrived at these conclusions. If you just want to be told what to do, you can skip it and dive right in here.
Your Siege generals will be the last PvP generals you invest rune stones and BoA on. This is because siege troops require gems to heal.
For Free to Play Players and Light Spenders:
I strongly recommend that you build only enough siege to fill your layers until a bigger, stronger, (and given the realities of the game), paying player whom you trust tells you otherwise. Siege is very hard to defend, having very low intrinsic HP. The only real way to successfully defend Siege is to have signifcant numbers of very high tier Siege, which means that if your defense fails, you give up lots of points. As a free player or a light spender, you are extremely unlikely to have enough siege to successfully defend your own siege from a big siege rally at this stage of the game.
As stated above, Siege Machines also require Gems to heal, outside of Battlefield. This will strain free players, and potentially even light spenders, for whom collecting the necessary gems to heal their siege is a challenge. That will influence them towards building siege machines in … insufficient numbers. See above. Its a nasty cycle.
On top of both of these points, building Siege Machines requires vast quantities of Stone, which is also required for your buildings. And you need to be growing your research buildings and rally spot much more than you need siege machines for the early and even, to an extent, middle parts of your growth cycle.