You and the seller should both agree on what the transaction should look like in the block chain. Once you see it show up (and assuming they didn't send the coins to someone else first!), you own the coins. There is a website for checking these transactions, but I'm told it doesn't handle valid transactions which have bitcoin change coming back to the sender. You can try that here: http://mastercoin.bysh.me:3000/

Edit: The link above often incorrectly reports MasterCoin balances (it has a bug which greatly inflates purchases for some addresses when they use multiple inputs) - using it for determining if somebody actually owns MasterCoins is not advised!