Migration Assistant will bring in whatever account(s) were on the old machine your migrated from if you check the box by that account name when you first run MA. So yes, if you made account Bob then ran MA with account Joe on the old machine, you will end up with the new account Bob plus the old account Joe (and all its data) on your new machine.
The best thing to do is run MA on the machine before you create any accounts, and just let MA bring in the old account and data. That way you won't have extra accounts.
So now you have two, separate accounts? If MA brought in your "real" account and data from the other machine, you can just login to that account and delete the new one your created.