Shipping settings in your PayPal account will only work with PayPal's own shopping cart, not with a third-party cart such as ours. You will need to set up Shipping Rules for your E-junkie account:
http://www.e-junkie.com/ej/help.shipping.htm
Here's a rundown of the basic steps you'd take to set up shipping with E-junkie that applies flat-rates within certain price bands based on the order total:
Go to Seller Admin>View/Edit/Delete Products:
Select an existing shippable product of yours and click Edit;
On the first screen, if Shipping/Buyer's Address is not checked there, tick that box;
Click Next until you can Submit to save settings;
Repeat this for all your tangible goods;
Leave Shipping unchecked for any non-tangible goods (e.g. ebooks);
When adding new shippable products, remember to enable Shipping/Buyer's Address.
Go to Seller Admin > Cart Shipping Settings and set up the following:
Shipping Origin: select your country and enter your zipcode (if you're outside the US, just enter any 5-digit number);
Shipping Destinations: if you will only ship to certain countries, select them in the list, or otherwise select nothing for Worldwide shipping;
Leave all other settings blank or 0.00;
Click Next to save settings and proceed to the Shipping Rules screen.
In the Existing Shipping Rules menu, select and Delete any Rules you may have saved there previously, so you're starting with a clean slate.
Set up a Shipping Rule for each Domestic flat-rate you will charge:
Shipping Rate Calculator = Flat;
Shipping Amount = enter a flat rate;
Country = Select your country;
Min. Item Total = enter the lowest order total that would qualify for this rate (you can leave this blank/0 when setting up your lowest flat-rate);
Max. Item Total = enter the highest order total that would qualify for this rate (you can leave this blank/0 when setting up your highest flat-rate);
Click Submit to save the Rule;
Repeat these steps for each of your other Domestic flat-rate levels.
If you will ship Internationally at different rates, then for each rate:
Shipping Rate Calculator = Flat;
Shipping Amount = enter your flat rate;
Country = All Countries (i.e. "rest of the world");
Min. Item Total = enter the lowest order total that would qualify for this rate (you can leave this blank/0 when setting up your lowest flat-rate);
Max. Item Total = enter the highest order total that would qualify for this rate (you can leave this blank/0 when setting up your highest flat-rate);
Click Submit to save the Rule;
Repeat these steps for each of your other Int'l flat-rate levels.
Click Back to Admin, and you're done! :^)