A wizard can add additional magic abilities to his bonded object as if he has the required item creation feats and if he meets the level prerequisites of the feat.

The cost to add additional abilities to an item is the same as if the item was not magical, less the value of the original item. Thus, a +1 longsword can be made into a +2 vorpal longsword, with the cost to create it being equal to that of a +2 vorpal sword minus the cost of a +1 longsword.

If the item is one that occupies a specific place on a character's body, the cost of adding any additional ability to that item increases by 50%. For example, if a character adds the power to confer invisibility to her ring of protection +2, the cost of adding this ability is the same as for creating a ring of invisibility multiplied by 1.5.

So does a bonded item already count as a magic item for these purposes?

If my wizard has a bonded amulet and wants to add a continuous mage armour effect to it, how much does that cost? I'm thinking it's 2000gp less the price of a masterwork amulet, but I'm not sure I'm right.

Well there are a few things that need to be addressed here. First off a bonded item allows you to craft an item without the need of the specific feats to do so. You must still have the correct level to make the item in question but if you wanted to make an amulet of natural armor to say which is already made. It would be the craft cost of the amulet of natural armor +1 , 1000gp. Lets say you wanted to enhance that item and add on additional effects those effects would also follow the same rules for crafting.

EX.
If the item is one that occupies a specific place on a character's body, the cost of adding any additional ability to that item increases by 50%. For example, if a character adds the power to confer invisibility to her ring of protection 2, the cost of adding this ability is the same as for creating a ring of invisibility multiplied by 1.5.

*******

Now the second problem is trying to defeat the system for example taking a magic effect and requesting it to be continuous to bypass the cost of more expensive items like mage armor protection
“If my wizard has a bonded amulet and wants to add a continuous mage armour effect to it, how much does that cost? I'm thinking it's 2000gp less the price of a masterwork amulet, but I'm not sure I'm right.”
You shouldn’t request a continuous effect if it has an alternative already presented in the chart

Armor bonus (enhancement)
Bonus squared x 1,000 gp +1 chainmail

Or bracers of armor +4 would be 16,000 gp

*** If a continuous item has an effect based on a spell with a duration measured in rounds, multiply the cost by 4. If the duration of the spell is 1 minute/level, multiply the cost by 2, and if the duration is 10 minutes/level, multiply the cost by 1.5. If the spell has a 24-hour duration or greater, divide the cost in half.

the rules for crafting

You don't EVER have to have the lvl, it just bumps the DC up if you do not.

The DC to create a magic item increases by +5 for each prerequisite the caster does not meet. The only exception to this is the requisite item creation feat, which is mandatory. In addition, you cannot create potions, spell-trigger, or spell-completion magic items without meeting their spell prerequisites.

Quote:

I'm thinking it's 2000gp less the price of a masterwork amulet, but I'm not sure I'm right.

Wrong.

The masterwork of an item does not count towards any magical bonus it has. What you are thinking is if armor has a +1 bonus (1k) and wants to be enchanted to a +2 (4k), it would cost (4k-1k) 3k more gold to enchant it upwards.

In 3.0/3.5 certain body slots required certain magical properties. In PF, that apparently has changed.

Mage Armor is a L1 spell cast from a L1 caster and has a duration of 1 hour/level. (1x1x1)=1 x 2000 for continuous = 2,000g base price.

Here is where it gets stupid:
You have to craft the spell onto the amulet (1/2). The amulet only works for you - if you take it off, the magic temporarily ceases to function and continues to not function until you put it back on. You have to be a wizard or a ?sage? sorcerer (that gets the wizard class feature), so it only works for your specific class.(30% (1-.3 = 0.7) deduction (multiplied into the 50% cost for crafting)

0.7x0.5x2000 = 700g to put continuous Mage Armor on your amulet according to RAW

Lets say later you want to get Shield continuous on your amulet as well.

Shield is a L1 spell with a L1 caster and 1 min/level duration.
(1x1x2) = 2 x 2000 = 4000g

0.7x0.5x2000g = 1400g. However, you already have mage armor on your amulet and these are not similar benefits. You always multiply the higher number by the 1.5.

1400g x 1.5 = 2100g. This price is in addition to the 700g for your Mage Armor, because Shield is a different kind of bonus.

Lets say later you put a +2 int bonus on your amulet.
2^2 = 4 x 1000 x 0.7x0.5 = 1400g x 1.5 = 2100g

And a few levels down the road, you decide to make the amulet +4 int.
4^2 = 16 x 1000x0.7x0.5 = 5600g x1.5 = 8400g

8400g would be subtracted by 2100g because you are improving the int bonus, not just adding a new feature to your magical item.

8400g-2100g = 6300g for the upgrade from +2 int to +4 int.

Item creation rules are pretty much entirely up to a GM. The Math in the above post is correct, but I don't think I've EVER met a GM who would actually allow that.