I'm currently running a 90w 4 channel Clarion amp on a seperate 750w Corsair power supply (needed a large supply since the amp draws approx 35-40a), but a smaller 20w/channel 2 channel amp should be able to be powered by the supply in your machine (check the power supply's ratings, and see what the 12v lines are rated for, a small 20wx2 amp should need around 10a or so, if your supply has better than 20a, and you're not using a bunch of drives or other 12v items, you should be good). I went with the Corsair because it has a single 12v 60a supply in it, and I knew the AMP I was running and the flipbook would be sufficiently powered without any issues (and it was less than half the cost of a 52a Pyramid 12v supply)...
I basically took several of the yellow/black wire combinations, and wired them together (just so I was sure I had enough copper to draw that the amplifier needed), and power the amp like that, same for the flipbook. I'm using that particular supply ONLY for the amp/flipbook though(a much smaller amp would be fine on the main PC's supply). I would still use the fuse that comes with the amplifier though, so as to not pull too much from the PC's supply. I would again also stress getting a name brand amp, as some of those cheap Ebay amps are grossly overinflated on their ratings, and are very sub-standard in construction..
If your existing pc power supply isn't beefy enough to power the amp and the PC, you can always use a separate PC supply, they can be modded so they switch on with the main system, or with another switch, so you could even play the machine without sound if you wanted.
I chose the amplifier I did because it had the power I needed, and a bulit-in crossover so that I could push just bass down to the subs, and cut the lower frequencies from the smaller upper speakers. I'm still playing with the crossover frequencies to get the sound where I want it, but right now it sounds much better than it ever did as a real jukebox (I converted an older CD juke over to a PC-based mp3 juke).