Ok, the "show vcc" and "show gnd" commands helped a lot. I've figured out how everything is setup to work except capacitor 1 and capacitor 2. I have vcc and gnd going to both capacitors but as far as I can tell from the schematic both of these are coming directly from the battery. This leaves me confused because if both vcc and gnd are coming from the battery, what's the point of the capacitors? I'm pretty sure I just don't know how to read the schematic.
So my question is, what component sends power to capacitor 1, and capacitor 2? The capacitor is storing energy to use when I push the switch, right? So then what component is the capacitor storing energy for?
I'm pretty sure the stored energy is not intended for LED 1,2,3,4 or 5. That leaves the microcontroler, and ICSP.
My Plan - I want to print the board design onto photo gloss paper and transfer it onto a copper clad board and make my own circuit board. Looking at the design in Eagle 5.6.0. I dont see how anything will work. I am planning on adding lines to connect GND and VCC to the LED's, Transistors, XTL1, Resistors, and Switch. Will this work? Then, I think all I'm missing is capacitor 1 and 2, microcontroller, and ICSP. With everything connected right on the circuit board it should all work when I solder in the parts, right? Am I on the right track?