One of the things you need to know is that when adding the shipping modules, the last MODULE you add and configure will show first in the shipping selection drop down list.  Within each module, the various options list alphabetically except for the UPS module as it offers hard coded selection not ones that you create and name.  For example, you add the "Flat Rate Shipping" module first and offer two selections: "Extra Economy $4" and "Express Overnight $20", then the "Quantity Based Shipping" second with two selections: "Absolutely Cheap $0.10 per item" and "Guaranteed 2 Day $5 per item".  The shopper will see the  selections as follows "Absolutely Cheap..." comes first, then "Guaranteed 2 Day..." then "Express Overnight..." and last is "Extra Economy...". 

As you can see, the two selections of the Quantity Based Shipping will come first since the module was added last and they list alphabetically.   Then the two selections of the Flat Rate Shipping come next again listed alphabetically.

  If you use the weight creatively, you can charge for shipping products regardless of their actual weight.   Let's suppose you want to offer a flat rate shipping of $5 on any purchase but you do not want to charge shipping for the purchase of Gift Certificates.  You can give all the products shipping weights and give the gift certificate the weight of zero.   Now if you configure the weight table to charge $0 for weights 0-1 and $5 for total weights of 1-9999 then that will practically make the shipping rates $5 for all purchases and $0 if buying the gift certificates only.

Another scenario is in case you want to charge per item BUT you sell packs of two or three and want that to be charged shipping as two or three units respectively.  You want the rates to be $1 for one item, $1.50 for 2 items and $2 for 3 items.  The quantity based shipping will not work since it will view the two pack as one item and charge shipping for one item only.  Creatively using the shipping weight and setting up the weight table will do the trick:

Configure it where 1 "weight unit" (pound) = $1
2 "weight units" (pounds) = $1.50
3 "weight units" (pounds) = $2

Then, make the weight of ALL products = 1 "weight unit" (pound) but make packs of  2 weigh 2 "weight units" (pounds), packs of 3 weigh 3 "weight units" (pounds).

Now when the customer checks out with (1) pack of 2 books plus (1) single book the cart   will "see" 3 pounds and charge  according to what's specified in the table  $2!  To add charges to certain items you can go to the product and click on the "Weight Table Shipping Charges" and put the extra charges you want.

  Notice that we are always talking about units of weight and not pounds, since whatever you enter in the shipping weight box for each product is unit insensitive, i.e. it could be pounds, kilos, items whatever.  It is in the store settings that you specify the text that goes next to it.  So, if you want to charge shipping by the ounce, you will need to put the appropriate charges for the weight table or the base + weight module and the value you put in the weight entry box of each product.  it doesn't matter what you put of text in the "store settings" even if you put the word pounds, as that is merely a text/label field and plays no role in the calculation.