If you know WHAT to address, a GUI based programming setup is the way to really get your car tuned. If you are unsure of what to do, leave it to the people who do or it will cost you more than a few custom chips.
Way back, I started doing my own because it seemed I couldnt get the perfect chip. One had this problem, another fixed this problem and had that problem. SO I did it myself, and I like to think I got pretty good at it. Ive since installed a FAST in my car so have nothing to do testing, so I dont offer chips to the public anymore. Add to that guys like Bob and Eric do some really cool stuff that I woujldnt know how to do in a million years, I gave up. With guys Like Joe Lubrant, Jay Carter, Bob Bailey, and Eric Marshall, I dont see why you'd want to chance hurting your car, unless like I siad, you know what you're doing.
