It should be perfectly safe, but the P6X58D-E is a triple-channel board and you bought two dual-channel kits. I mean, it would have been better to get a triple-channel kit (such as a 3 x 4GB kit, or a 6 x 2GB kit). Not only would it probably be easier to overclock three or six memory sticks on a triple-channel motherboard as opposed to 4 sticks, but do you really need 12 GB of memory? Some people do, but then there are those who don't and don't know it. So I have no choice but to ask because I have no way to know for sure.
So what you'll have is a triple-channel setup with 1 extra stick.
Now, if by chance you got those two dual-channel kits from Newegg at those prices, then that would mean you paid $154.98 shipped. So, here are some 12 GB triple-channel kits for approximately the same final cost or less:
Now, here's Newegg's inventory of 3 x 2GB kits sorted by price highest-to-lowest:
In other words, if you can return those two dual-channel kits, then I recommend it because then you could use that money to get a nice triple-channel kit.