using two P2 cards
 

When using two P2 cards and a shot spills over onto the second card how do you make that into one clip on your editing program(Vegas for example).

On an editor that understands the MXF file format, it's done automatically for you.

On a system like Vegas, it doesn't understand the MXFs at all, you have to convert the MXF files into .AVI files. Which means you have to manually take the two chunks of footage and butt them together on the timeline.

If you use EDIUS or Avid or FCP, they all know about multiple clips spanning multiple cards and can deal with it seamlessly.