First, I'll refer you to our Shipping help page here:
http://www.e-junkie.com/ej/help.shipping.htm
If you could explain what you want for shipping charges, we can give you more specific instructions to set that up. A good rule of thumb with our system is to consider what you actually want to do first, then just look for ways to accomplish exactly that (rather than trying to understand how the whole system works first, which can quickly get a bit overwhelming). I'm not quite sure what you meant about setting up shipping for individual products vs. using Cart Shipping Settings, since they actually work together, so I'll attempt to explain that here:
When you add/edit a product in Seller Admin, you can enable the "Shipping/Buyer's Address" setting for that product. When that item is added to a buyer's cart, that setting will trigger collection of the buyer's address during checkout. Shipping calculation will include all items in a buyer's cart which have Shipping enabled.
When you enable Shipping for a product, a following screen of settings for that product will let you specify a shipping weight, a packaging container type, and a packing capacity (how many units of that product will fit into the selected packaging type). These work together with your Cart Shipping Settings to determine the actual shipping amount that gets calculated.
In your Seller Admin > Cart Shipping Settings, the first screen lets you specify a Shipping Origin (your country and ZIP/postal code), any specific Shipping Destinations (if you will only ship to certain countries), an optional Handling fee (which gets added just once to each entire order which uses shipping calculation), and optional weights/costs for various packaging container types. Clicking Next saves those settings and takes you to the Shipping Rules screen.
Shipping Rules will enable Shipping calculation methods for each order based on the buyer's location and/or the size of their order. The USPS and UPS methods simply take the total weight of the order (item weights + any container weights used to package those items) and the buyer's destination, then submits that data to the USPS or UPS rate-lookup site to obtain a rate. Other methods allow you to configure the calculation manually, such as a shipping price per item, or price per unit weight, or a flat rate per full order.
Rules with more-specific locations will override Rules with broader locations, so e.g. if you have one Rule for "All Countries" and another for "United States", a buyer in the US would only qualify for the latter Rule. If a given buyer's location and order size qualifies for more than one Rule, their cart will show a choice of shipping options for the buyer to pick.
