Go to your Shipping Conditions and Methods area and click on "Add Method".

YourDomain.com > Modules > ECommerce: Products (Mx) > Shipping Conditions/Methods

Once you click on "add method" you will see 2 drop down boxes.  Choose the Condition you would like to apply this method to, and Choose "User Defined" in the "Service" drop down box. (click here to see more about "Conditions")

see screenshot:

Next Click "Add"

Then you will be taken to the methods details page.  This is where you can select what type of shipping method you are going to use.

see screenshot:

Next since there is no auto calculation done with a user defined method you will want to either specify "Free Shipping" or setup a calculation or flat rate in the range area in the bottom.  

You can additionally put customer notes here, and specify a markup if you wish.  Specifying the "Package Type" can change the estimates for your customers.  Try to pick the most accurate package type.  You also need to be sure each of your products reflect an accurate weight so the estimate is as accurate as it can be.

 
Shipping Charges table allows you to define a cost to ship an order based on its cost or weight (depending on Ranges by option above)

This formula is used: Shipping Charge = Flat + [Order Cost]*% of Total + [Number of Items Ordered]*Per Item + [Order Weight]*Per Lb

Flat - specify an amount using this field if you want orders to be subject to a flat shipping charge regardless of the number of ordered products or their weight or cost.
% - type in a value into this field if you want the shipping cost calculated as a percentage of the total cost of products ordered.
Per Item - specify an amount using this field if you want the shipping cost calculated based on the number of items (quantity) ordered.
Per Lb - specify an amount using this field if you want the shipping cost calculated based on the weight of products ordered.