I am reading up on Mastercoin, and I must say, it is quite confusing. Am I correct in saying that your Bitcoin address is your Mastercoin Address? If so, I have one private key that contains two cryptocurrencies?
Have a look here: www.youtube.com/watch?v=mAW-kuoZaHU and you'll probably understand how it works.
You download the blockchain with Bitcoin-QT and run my Mastercoins wallet through it.You label the addresses in your QT wallet and you can now send BTC and MSC to these addresses.