If you can get a 2012 Focus for around invoice without additional fees you're doing okay. The whole marketing assesment and fuel is charged from Ford, not from your dealer you are buying from. This is a non-negotiable item and advertising varies by region. This helps pay for all the Swap your ride ads on TV and so forth. A SEL sedan will have about $650 worth of holdback in it so if you must, see if they'll back out the $346 out of the price.
However, if their inventory is low and they are not expecting much in, you might be stepping over a dollar to pickup a penny. Especially if they aren't charging shipping to get it from the other dealer. We typically pay on average $900 to do a trade if it's out of state.