"I want to add Archangels (in the raws of DIG DEEPER) as megabeasts to the game. Now, the thing is, I don't know how I'd go about doing this in a way that would be appealing. For example, I want them to be human sized, but that would take away a lot of their fighting power, so I'll up damblock instead." Alright, to do this you just need to increase the DAMBLOCK and the amount of damage their attacks do. In terms of their carrying capacity, they'll have the same as a human's. In terms of opening a can of whoopass, they'll be a lot more capable.
"Would adding an entity entry for a civ of Archangels allow me to arm them with weapons and armor? Also, if they have a civ, will they still attack fortresses?" This won't work as you intend. Let me explain why: Basically, the civ creatures won't be [POWER] creatures really. They may well worship one of their own kind, however. The [POWER] being worshipped will probably not be armoured or clothed.
"Will they attack fortresses even if they have the [BENIGN] or [GOOD] tags?" These tags are more to do with environment than behaviour. The Good token restricts them from appearing in Evil areas, and the Benign restricts them from appearing in savage areas. The nature of the creature itself is irrelevant.
"Also, how do I ensure that they end up getting the worship of lesser, non-evil races? Do races only worship if the spheres align?" This is correct, yes. But from what I can tell, the alignment only needs to be partial.
"Come to think of it, I'd appreciate it if someone could direct me to a modding guide that could help me with these questions. The one in the wiki is inadequate." I'm on IRC a lot. Come ask questions.