Step #1: download and install media center master.
Step #2. Do step #1 before anything else.
Seriously, Try this:
After you install MCM first get the folder structure right. Make sure you have first a "dexter" folder that inside it has everything dexter. That means you will have additional folders inside it called "season 1". "Season 2" etc....
You must have all your season 1 episodes inside a folder called season 1. That season 1 folder is inside your main dexter folder.
MCM should take care if the rest. I'm a big fan of the paid version, as it will auto rename everything properly. As long as your structure is right and it can read the "s01e01" in the name it will download all the metadata and art and rename everything properly.
You will need to play with the settings of MCM. Put it on XBMC mode (I use media browser) if that's your choice. Also choose TV mode if you are doing episodes and not movies.