Yeah like JarJar said these relate to each other in no way possible
Pokegen (and variants) are programs used to create Pokemon and send them to your game via GTS. These Pokemon are 'hacked' and are not allowed to be used in any sort of official tournament and stuff.
RNG Manipulation on the other hand is perfectly legal, as it abuses your Ingame ID, and allows you to get IVs that you want (But it takes really long and stuff). You can click here for Smogon's RNG stuff. You can use Pokemon affected by these in whatever the heck you want