Thanks for the replies. I have it working but its not at full brightness (mostly because of transistors instead of mosfets), also I have a lot of problems with connections failing and tracking them down is a pain. I don't have the soul to take it apart and replace the transistors but I might at some point. Also apparently my circuit has some other issues which were discussed on one of the LED blinder threads I started. I know that these problems are mostly my fault due to the fact that this was really my first big high power project. I just think it would be awesome to have a little board with like a terminal block on each side (one side power & ground in, other side power & ground out and on an adjacent side the 3 pwm inputs) so that they could be sort of daisy chained and all of the necessary components onboard. I might draw up a circuit diagram based on your descriptions and have you check it over.
Be aware if the PWM duty cycle exceeds a certain limit, the whole thing goes up in smoke and people will run screaming into the night.
What happens if they are at 100% duty cycle (aka fully on)? Would they burn out?
Plus the way I have it set up has for some reason burnt out 2 of my beloved arduinos 
I ordered a new atmega328 from ebay and I'm hoping it will fix the problem so I don't need to buy a whole new board