1. Whoever you saw plugging a 6-pin connector into the CPU-power plug did not know what they were doing. There is a reason they are different and you stumbled on that reason.
2. The fact that everything still works is very surprising, but I wouldn't be surprised if you drastically shortened the life of most of your parts, especially the one that produced the smoke (guessing power supply). If there was smoke, something burned up, and something isn't operating like it should anymore, and that is likely to be the first thing to fail (and possibly take the rest of your system with it).
Sorry to be so glum, but plugging a 6-pin connector into the 8-pin spot was just a bad idea. Next time please, please just ask questions before you charge ahead. Even if you think it's a stupid question it's still better to ask, we are happy to help. I really hope it keeps running for you, but I would be ready for it to die anytime.
Good luck man.