1. You've mentioned that flat rate boxes are $13.60 & $18.85 for the med and large. It appears you are paying for postage at a post office as those are retail rates.
Use eBay labels instead as the rates are cheaper. Commercial Plus is $12.05 and $16.55.
Its also much faster - just drop the packages off. Time is money is it not?
2. Get a monotone laser printer to print labels on plain printer paper - two to a sheet. Make sure the laser printer has a separate drum and toner cartridge so you do not pay for replacing the drum every time you replace a cartridge. A large capacity cartridge will print thousands of labels. By paper by the case - a local store has rebates on such paper here resulting in a cost of just over a $1.00 a ream.
Don't use a inkjet. Ink costs way more.
3. Get a USPS online account and order various box sizes, envelopes, etc... - Regular Priority, Flat, Regional, etc...
4. When printing labels be sure to check alternatives such as regional, which you can't specifically add to a listing.
5. Invest in some software such as GarageSale (Mac) and then use calculated shipping.
Create a series of reusable templates based upon shipping scenarios that you then simply duplicate. A single template could by default list rates for regular Priority Mail, Parcel Select, and a Flat Rate Medium box, which will all be displayed to the buyer for comparison since flat rate boxes may or may not be cheaper than regular rates depending upon the destination zip code and weight.
Don't use fixed or free shipping unless you've got some experience under your belt. Can you look at a item or simply place it on a scale and in most visualize in your mind how it should be packaged and what the given packaging is going to add to the basic item weight? If not, then don't try using flat or free as you will get burned financially.
Assuming you were to use GarageSale one could create templates for 8 ounce and under packages and 9, 10, 11, 12, and 13 ounce packages. Because eBay will incorrectly shows a Priority Mail rate for First Class Packages at the 14 to 15.999 weights create a single template for those weights using a flat rate of your choice which is at least $4.30 (update this price as shipping prices go up). This way customers will not see eBay's higher priced mistake and instead see a lower cost and be more likely to buy. You are now done creating any First Class shipping templates and all you need to do is duplicate one of those template and add specific item details. Perhaps work on just 1st Class for while until you know it like the back of your hand?
You can of course customize further. Lets say you regularly sell a particular collectible that ships out via 1st Class Package Services and all these items share commonly repeatedly information. Create a second set of 1st Class Package templates like the first, but with that repeated information already filled in.
Here's part of a sample book template that uses a css generated table to easily display common traits shared by books. Instead of typing in "title, author," and so forth for every book its already completed.
6. Obtain free boxes from local store for shipping Parcel Select & Media; creating inner shipping boxes or wraps; creating outer wraps; spacers; corner and sidewall reinforcers; etc...
7. I frankly only use the padded envelope if I can first pack the item inside a box or cardboard sleeve and insert it into the padded envelope in an effort to simply save on the shipping rates. The padded envelope provides little protection at all on its own. Keep in mind your item may have other items fall on it during the sorting process and be tossed into carts - seen both.
