Oof. You've asked quite a few questions in that thread. Let me start with a tl;dr - Planar Conquest is based off a rule set that Wizards of the Coast created. It's called Open d20, based on WotC's d20 system. If you really want to get the details, then you should check out the website
http://www.wizards.com/default.asp?x=d20/article/srd35 and just go to town on the reference material. That said, I'll try to answer your questions as briefly as possible while still giving you the details you need.
You ask several questions about saving throws. In brief, there are two major combat mechanics in d20 - attacking something directly (sword, arrow, wand, etc), or attacking something indirectly (magic spell, special ability like a basilisk's stoning gaze, etc). Direct attacks are protected against by armor (Armor Class); indirect attacks are protected against by saving throws (Reflex, Will, Fortitude). The type of indirect attack determines what saving throw is applied. Elves are classically quick and frail, thus they tend to do well on Reflex saving throws but poorly on Fortitude saving throws. So throwing a ball of fire at them, they can maybe duck or dodge, and they make a Reflex saving throw. But attacking their well-being by surrounding them in dark energy (Spit of Bile, for example), they don't do so well with, because they're not too tough. Dwarves tend to be the opposite.
Die rolls. The core mechanic of d20 is random die rolls. XdY+Z is the general format. X = number of die to roll. Y = sides on the die. Z = additional modifier. 2d6+4 gives a range of (2-12)+4, or 6 to 16. d3-1 gives a range of 0-2.
What does Armor Class actually do? When a unit attacks, it rolls "to hit". I'd like to refer you to an explanation I gave on antoher page to save typing time, if you don't mind.
http://forum.wastelands-interactive....critical-range
Effects of Berserk Fury. Berserk Fury doubles your damage done, so your archers (1d8 damage from their bows) would do (1d8)x2 damage if they hit. It also increases the damage received by 50%, so if you would normally take 10 damage from an attack, you take 15.
Good enough, or need more?
EDIT: Oh, Difficulty Class. DC is essentially the attack roll for an indirect attack. For a normal attack, you would roll d20 and add your hit bonus, then compare that roll to the target's Armor Class. DC, used for indirect attacks (as I described above) is the value you compare to the target's relevant save. A weak spell like Flame Arrow, early on, might have a DC of 12. Flame Arrow is defended by Reflex save. You roll a d20 and add your Reflex bonus to that - if you have a +2, then you'd need to roll a 10 or better, giving you a 55% chance to resist the spell in some way. Spell description will tell you what the effects of a successful saving throw are - in the case of Flame Arrow, you take half damage. Just to make things more complicated, some units (a lot, frankly, in Planar Conquest) have Evasion, so if they make their save, they get an extra bonus; they take no damage, instead of half. A well-boosted Wrack, later in the game, might have a DC of 29. Wrack is defended against by fortitude. If you had a Fortitude bonus of 9, you'd need to roll a 20 to succeed. 5% chance.
SECOND EDIT: Huh, that WotC page no longer works. Sorry to give you a bad link. I'll leave it there just in case it's a temporary thing. It used to work, as recently as a couple months ago.