I decided to fix up the board design. I added a jumper underneath the 328P socket, but I added all the holes for the unused pins on all the DIP sockets, so no more cutting off pins! :)
REMEMBER : This view of the board is the BOTTOM, so all the components go on the other side, and that means you have to watch out for pin 1 on all the ICs! It's a little confusing, even for me. I just hold the board like it looks below and hold the IC in the air, as it were going to match the image, and then flip the two over, and it should have the proper orientation. It also helps a lot to watch for the pin 1 indicator; the indentation in the sockets.
The reason I designed the board like this is because it makes it easier for me to manufacture the boards. I mill them out, and of course the side you mill has to be "up", so this way I don't have to reverse the file when I export it out to the routing program.