Gene manipulation in any artificial form is bad
Wow, what a generalization. This is 100% incorrect.
One is a natural process other is guess work
Incorrect. Genetic modification is not guess work. Have you ever been in a laboratory involved with genetic manipulation? It's not total guesswork - I can go into detail on this for you if you wish. For a large portion of what do, we know exactly what we're doing and why. I urge you to get read more on the subject (e.g. Further topics on Genetics, Bioinformatics, and Biotechnology).
Also, there are MANY natural ways for genetic material to be inserted in the genome of another organism. "Genetic manuipulation" occures naturally too. http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens
The code, is a long string of code, but out of that code sections are termed "junk dna" this dna does other stuff that we don't actually know
Yes, they are termed "Introns" and defined as regions of "non-coding DNA", DNA that is not used to synthesis proteins. However, the vast majority of genetic manipulation occurs in the "Exons", the DNA that does code for proteins (and regulation of transcription and expression of the DNA). Exons are well-studied and for the most part well understood (although of course, there may be areas that are less studied/understood than others, but the generalization of total "guesswork" is so unbelievably incorrect)
You sound like someone with very little knowledge of Genetics, so I understand where some of your misconceptions may arise from. I am more than happy to to further expand on anything or point you in the right direction to learn more if you wish.