To get your clips to work you need to re-encode them in a program like virtualdub and use a codec like Huffyuv or Lagarith
Its best to encode only the clips you need insted of whole episodes since those codecs can make HUGE files
you can download virtual dub here
http://prdownloads.sourceforge.net/virt ... p?download
Since you are using downloaded footage at some point you may get files in MKV or OGM format. For those you will need virtualdub mod to convert them
I used these screenshots to show someone how to convert dvd vobs but they can be used here for this.
The screenshots are from virtualdub mod but what you are doing can be done in regular virtual dub
run virtualdub mod (or virtualdub) and open the video file wherever it is on your hard drive
After it opens go to "video" then select "compression" and select a codec like Huffy
You can use the buttons like shown below to select scenes you want to encode.
Once you select a scene go to "file" then save it as an avi.
Thats basically what you have to do! ^_^