I recently ordered Homm2 Gold, and MM6 packs for 20 dollars on friday, and as I went to pay, my card was rejected for being a foreign area I'm ordering from.

I got a phone call on monday asking to approve it, which I did. So, I waited for a while, and my order was still pending in my account, so I assumed I needed to just place the order again, and it will work this time. I was wrong, so now I have two pending orders. Will it double charge me for them, or will the second order disappear once I get them the first time?

I'm very confused about this, being a new card user.

Pending? You mean when you view your order history? It does not matter what is showing there as pending, that will vanish after some hours.
If you have two pending orders there, it just means you wanted to buy these things two times and both times did not continue the checkout / payment.

When you want to buy something, it needs to be in the cart and at the checkout you can see what is in it and what you are paying for. And you can't buy the same games twice for yourself, so there shouldn't be any problem

I'd contact the appropriate support and cancel the latter order to be on the safe side. Cancelling is generally easier than getting one's money back, although I doubt GOG will cause you any trouble on this. However, you never know.