A few tips:
1) Use the calculated shipping feature. It is the most fair and accurate method.
2) Watch your handling fees - avoid adding them at all. Add handling fees on to the price of the item instead so the buyer does not feel "swindled." (Many buyers on eBay are not business people and are clueless about the cost of doing business. We have to cater to that to get good DSRs.)
3) Avoid using USPS Flat Rate boxes. They are easy by design, but are not always the best choice.