Well, part of that is MP vs SP. The AI is not smart enough to block an ST with a Scout!...then just send in two siege towers, and Austria was bottom military, but his blocking scouts and comp bows made mincemeat out of the towers and I retreated with the army.
Did you actually loose a ST? I should think they hold up to CBs no problem. I am not surprised you were forced to retreat, no shame in that when facing a human opponent!
In my experience, the bare minimum number of ST is three. For the GotM, I will be waiting until I have four for my late push. You need at least one spare so the one in front can retreat for the next assault. You need to keep two on the front line all the way to the city -- so they can buff each other.
But is it not an odd and wonderful feeling to be using siege units to screen archers?
Also, even if your first push is not too successful, be sure to get Cover II on the ST (which is not hard, just put them near barbs, or build a barracks). It is pretty rare to have Canons and Arty with Cover II (since it normally comes with a high opportunity cost) but it is actually quite helpful against city garrison and frigates (and later, my bane, planes).