Not sure, I follow. You paid the ETH to buy EOS, using which wallet, Metamask or MyEtherWallet?

The wallet that you sent the ETH from to get EOS, is the Address where you have EOS. Next, you need to use that wallet, to register your public key, also you need to do a third transaction to claim your tokens from that wallet. Without claiming tokens, your EOS will not show up, even though they are inside the contract still. They are not automatically sent out when a window closes, you have to process a transaction to claim them using gas.

To do all this in metamask, just take your MyEtherWallet private key that is in that system, and metamask will let you load up other accounts into MetaMask using a private key. Very likely, if you login to the EOS.IO system using the correct account that the ETH was sent from with MetaMask, the "Claim Tokens" button will be highlighted, letting you claim the tokens.