You've got weapon enhancements figured out, it sounds like.
Armor enhancements only increase the AC bonus of the armor. Nothing else.
The masterwork quality does decrease the armor check penalty of your armor, but only by 1.
Masterwork armor reduces the armor check penalty. It can only be masterwork "once" (i.e., you can't make "masterwork masterwork chain mail", just "masterwork chain mail"
A special material can alter the armor's hit points (its own, for defense against sundering), hardness, and weight at a cost.
Enhancement Bonuses only add to the Armor Bonus of the Armor, or the Shield Bonus of a Shield. Like weapons, enhancement bonuses on armor can only go up to +5 -- but you can add other powers that are priced as if they were enhancements up to a total of +10 (combined Enhancement and non-Enhancement abilities, and at least a +1 Enhancement is required before you can add anything else). Other abilities that are priced as gold only can be added as much as you can afford.
A Masterwork Weapon confers a +1 Enhancement Bonus to Attack Rolls, and costs an additional 300 gold (plus the item's base cost) to craft. If you're making it out of Special Materials, you also add in that cost as well to the base price (though some materials automatically apply masterwork quality, and the effects and costs for such are factored into the special material descriptions).
A couple examples are a typical Longsword, which costs 15 gold, a Masterwork Longsword, which costs 315 gold (300 masterwork cost + 15 base cost), and an Adamantine Longsword, which costs 3,015 gold (3,000 Adamantine material cost + 15 base cost, Masterwork cost is already factored into the 3,000 material cost, so you don't add that in).
Armor is mostly identical, though the cost varies (Masterwork is only 150 gold, and the cost regarding Special Materials depends on the category of armor you're making), and it reduces the Armor Check Penalty of the armor in question by 1 instead of granting an Enhancement Bonus to Attack Rolls.
A couple examples are a Chain Shirt, which costs 100 gold, a Masterwork Chain Shirt, which costs 250 gold (150 masterwork cost + 100 base cost), and a Mithril Chain Shirt, which costs 1,100 gold (1,000 Mithril material cost + 100 base cost, Masterwork cost is already factored into the 1,000 material cost, so you don't add that in.)
Regardless, a weapon or armor must be Masterwork in order for it to be made Magical (whether it's through crafting it normally, or having it made from a Special Material to count as being Masterwork). Magical Weapons and Armor always start off with a +1 Enhancement Bonus; this applies to Attack and Damage rolls for Weapons (doesn't stack with the Masterwork bonus), and to the AC bonus for Armor. This amount can be increased to +5, and cannot exceed that amount except in special circumstances (such as a +4 Bane weapon against a designated foe).
Until your weapon or armor has a +1 Enhancement Bonus from being magical, you cannot add any form of Special Abilities (such as Keen for weapons and Ghost Touch for armor). Each special ability has an Enhancement Bonus "cost," and this cost usually equals "+X," X being the number that it lists.
You then add all of the Enhancement Bonus "costs" from Special Abilities and the actual Enhancement Bonus of the weapon or armor (minimum 1, maximum 5), and then consult the chart to determine how much it would cost to have that weapon or armor created (either from scratch, or adding onto an existing weapon or armor). Keep in mind that the reason the chart only lists +1 to +10 is because +10 is the hard cap. You cannot have a weapon or armor that has more than +10 in terms of enhancements (both bonuses and properties), and you cannot supersede that limit in any way per the rules.
Once you calculate the value of magic and the value of the base weapon or armor (standard cost, masterwork quality cost, and material cost, if any), you add them all together, and you have the total value of the weapon.
Here's an example:
Let's say we have a Fighter who wants a +1 Keen Cold Iron Longsword. We first have to start with the weapon to receive the enhancements, which would be a Masterwork Cold Iron Longsword. A Longsword's base cost is 15 gold, a Masterwork Weapon is 300 gold (which you pay since the material we're using doesn't include Masterwork costs). This totals into 315 gold. However, because it's made of Cold Iron, this means we follow the Cold Iron entry, which states to double the cost of crafting the weapon, which results in a weapon costing 630 gold.
Now, let's say we want to make it Magical, by granting it a +1 and applying the Keen weapon property. Because we used Cold Iron, the description for Cold Iron states that turning a Cold Iron Weapon into a Magical Weapon requires an additional 2,000 gold, which means this is a flat cost added when we first enhance the weapon (as future enhancements don't entail this added cost). A +1 Weapon costs a +1 Bonus, and Keen is a +1 Weapon Property, which means we have an effective +2 Weapon. The chart for Magic Weapons states that a +2 Weapon costs 8,000 gold (not including the 2,000 gold surcharge for using Cold Iron).
So, we take the Masterwork Cold Iron Longsword's cost (630 gold), add it onto the cost given to us by making it into a magical +2 Weapon (8,000 gold), as well as add a 2,000 gold surcharge due to the material we're working with. 8,000 + 2,000 + 630 = 10,630 gold.
The +1 Keen Cold Iron Longsword gives the Fighter a slew of benefits:
-Counts as Magical and Cold Iron for overcoming Damage Reduction and other effects due to the material being used and the enhancement bonus being added
-+1 to Attack and Damage Rolls for using the weapon to attack enemies
-Threat Range is doubled from 19-20 to 17-20, sparing both a feat and improving overall combat prowess
Now, let's say he wants to turn it into a +2 Keen Cold Iron Longsword. He takes the cost of the new weapon (20,630), subtracts it from the cost of the old weapon (10,630) to determine how much it would cost to improve it; in this example, it's 10,000 gold. This applies if you're wanting to improve the enhancement bonus of your weapon or armor, or even adding special abilities to your weapon or armor.
I hope this answers any questions or concerns you may have had regarding magic items.