You can add validation to the checkout form to ensure that the user selects a country before proceeding. If you have either CSS Form Builder or Validation Toolkit you can apply either client side or server side validations for the checkout form country selection. If the user does not select one you have have an error show letting them know to select a country. If you have either of these products you should try running the validation wizard on your checkout page.
As for a guide or reference to help you make sense of the charge rules here is a link to one that references the Blue Sky store:
This is for discounts but the concept and interfaces are the same for shipping, tax, and charge rules. The only difference between these and a discount rule is that discount amounts are subtracted from the total and charge amounts are added to the total. Please post back with any specific questions that you have about any part of this and I will help you with whatever I can.