Different amino acids do slightly different things, but all tend to contribute to building muscle so basically if you take a mix, say BCAAs with arginine and lysine, better lean muscle mass development will follow as opposed to just BCAAs.
One method that seems to be working really well that I have just been reading up on (and the reason for me only mentioning the ones above) is taking arginine with some lysine in the morning on an empty stomach at least 1 hour before eating. Then take your creatine and BCAAs and protein or whatever stack you are using after your session.
Main thing is a healthy diet though, otherwise the effects of supplements are reduced.
Also, taking ALL amino acids is pretty pointless. Like protein, your body can only process some much per day. And all amino acids are absorbed the same way, so to simplify things, the amino acids are competing with each to get into your body. The best thing to do is to narrow it down to a small batch you think are best for you and use them for 2 months, then have a month off, then try some different ones for 2 months etc etc, cycling like this is good also is it gives your kidneys and liver etc some time off to keep up with all the extra substances they have to filter/process.
If you do hit the substances hard make sure you drink HEAPS of water 3-4 Litres a day. At first you will be pissing heaps (especially with certain aminos as a few boost your urea cycle) but after 2-3 weeks your body adapts to it.