You only need one configuration, and that configuration needs to be one that works for your setup. That should answer it..
If not, here goes second time: it doesn't matter. All that matters is that the configuration works, your X starts and you get the desired resolution etc. If the nvidia-installer-created xorg.conf works flawlessly for you, go ahead with it - if it doesn't, you need to modify either it or your original configuration, so you can throw a coin to decide if you want.
If you have never touched xorg.conf before, you can just as well use a newly generated one (the nvidia-generated one). If you have customized your xorg.conf, you might want to keep it that way and just make the few modifications nvidia driver needs (I think this is easier; you know the base config works, just add some things -- if you use the nvidia-generated one, you don't know if it works before you try) and live with it.
Do it the easier way, whichever it is. Take backup of the original, try nvidia config, if it doesn't work then put back the original and modify it.