The current account is the difference between exports and imports. Atm America imports more than it exports hence the current account is in deficit. Importing more ethanol will increase the deficit.

This argument is pretty useless in regards to ethanol though, given the large comparative advantages enjoyed by some producers compared to inefficient American corn ethanol.

I know what current accounts are, I just never had anyone explain to me why its a problem.

If we import (rather than locally produce) Ethanol, presumably it displaces imported oil, or oil products. Assuming we only import ethanol which is actually cheaper than the oil it replaces that would be a net reduction of imports. But, probably more importantly we would have more farm produce to export. It sounds to be like either win-win or maybe draw-win.