Calculations work just like columns. Once you have added a calculation you can just drag/drop it into your cart display wherever you want it displayed just like you would any other column.
The calculations can be used for anything you want. Adding calculations can be done for any reason. The only one that will actually effect the price is the TotalPrice calculation. The others can be used to supplement charges or display values when you want but won't actually be added to anything automatically.
I was referring to removing the surcharge calculation from the TotalPrice and setting it back to Price*Quanity, which it appears you have.
If you go to the shopping cart object definition and click on the "Charges" tab, you can add a charge and set it to the total of the Surcharge calculated column.
You don't need to re-run the wizard, you can just update the "Store cart details in database" server behaviors on the confirm.php page and the pp_confirm.php page (if using express checkout).
I try to give free outstanding support through the forums. That is what I'm trying to give you, but may not have the skills that Jason had to satisfy your queries instantly. I can only do my best, and I apologize if it isn't as good as you have come to expect from Jason. He is truly the best.
If you want to do things more quickly however, we can do hourly premier support where we do screen sharing and actually help build your application for you hands-on. An hour of premier support would have certainly saved you the time you have struggled with this so far, but I'm happy to keep trying to explain it to you here as best as I can.