When you purchase cards they are put into your inventory. When you are ready to ship you pay a flat $3 for standard shipping. If you haven't switched over to Advanced mode (for flipping - you have to go into your settings to do this), you've already paid the .25 per card processing fee and when you ship out, it will be at $3.00. You only pay the .25 extra per card at shipping time if you are in Advanced mode.
A vast majority of the cards are hosted in Redmond, WA - so they are all in the same physical location. COMC is a consignment service - I send them cards which they scan and get ready, I then price it. When it sells, they package it all up and send it for me.
Right now through Monday, if you purchase at least 20 cards they are shipping them for free. Plus, you get a scratch cards for each 20 cards that could allow you to win free credit and other prizes. You also get a $5.00 bonus back for every 100 cards you ship in a month.