Hi there~welcome to the world of selling on eBay. I quit using the shipping calculator about six months or so ago. It was never really accurate, and the USPS rising prices often made shipping prohibitive. It does depend on what you are selling, however. I sell a lot of pottery & glass, so my boxes tend to be heavy. I do use my scale to get the proper weight, and then I use the USPS web site's calculator and base a cost to coast estimate. I've been using flat rate shipping with fair success.
As far as payment is concerned, soon we we will only be able to accept Paypal or another form of electronic payment (can't remember the name), and we will no longer be able to accept money orders/checks.
Best of luck!