If you didn't receive any confirmation E-Mail from Stardock, then it's a relatively safe guess that it didn't go through or you didn't order it the first time... Buuuuuut, this is money we're talking about, so that does nothing to alleviate the worries you may have about spending 50 dollars too many for a game you've already paid for.
Best thing you can do is call Stardock Customer Support first thing in the morning and see if they can help you.
Edit: Make sure to make it clear, in the case you -did- order twice, that it's the Limited Edition you want and not the original. Ya can't be too safe. =P