I'm currently using 5.4, and right now there is only one generic account inwhich all additional costs are posted to.  I have to do an analysis each month and reallocate these costs to the correct accounts.  Is it possible to have a gl account defined within the setup of the additional cost?

Yes, when you setup various PO additional costs you can link them to a specific GL account if you like.  You can also change the GL acct for the additional cost as it is entered.

I'm not clear on what I want to accomplish.

We receive container shipments and would like to incorporate some of the cost of offloading.  So if I want to charge a 2% handling/offloading charge on all container shipments, how do I set that up as an additional cost.