Carputer/Car PC install and amp question

I don't like to settle, so instead of getting a headunit that does some of the things I like, but not all, I figured I'd just build a computer that does everything I want, and more. Got it all purchased, the computer parts put together and working, now comes the install(which is looking more and more daunting as the temp drops)-the computer stuff is easy, I'm good with that stuff, wiring it all in, piece of cake, where I'm not quite sure on is the audio.

The question I have is this- I have the III with the jbl amp- does it make sense to use the Pac-tato and run the sound from the pc to that through the system(seeing as it's all bascially setup in the car that way), and 2- if anyone has ever done this, have you had any problems with the amp "popping" when you turn the computer on. I know from other forums it's an issue with other cars with aftermarket amps-
The power supply I'm using has a connection on it that is meant to delay the On signal to the amp, so it doesn't do that, but looking over all the wiring diagrams I'm not quite sure if there's a way to integrate that, or if I even need to. http://resources.mini-box.com/online/PWR-M2-ATX/PWR-M2-ATX-manual-engl.pdf is the link to the power supply unit. Page 2, in the diagram, the J6 connector, and there's a little blurb on the next page to perhaps help with some more info. So, anyone with experience, I'd love the chime in, or anyone who has any insight on the above, let me know what you think. I'll post picks and more specs as the actual install goes along. Thanks