Back when I had a vehicle that had a clutch, and kept crapping clutch plates and/or throwout bearings, I had the flywheel turned a couple of times. I used the same machine shop both times, so as I say it's a limited experience.
They used a setup that surprised me, which is why I decided to mention it here. They mounted the flywheel on a lathe, but as a tool they had a motorized grinding wheel setup and they actually ground the flywheel as it spun on the lathe. This produced a very smooth to the touch surface, but with just enough roughness that it helped the 'break-in' of the new clutch plate very nicely, much like a light sanding of a disk brake rotor does for a brake job.
They were able, in a single pass, to resurface the flywheel very nicely this way, and the surface was still fairly good the next time I had to replace a pressure plate (along with a new clutch plate and throwout bearing. It was a small, low end sports car, and I drove it like a porsche!)
At any rate, I have to agree with Doc, spend a few extra bucks and go to a good machine shop. Places like O'Reillys frequently have very little training on something like that, the extra cost is worth it for the job well done by someone who has been doing it for years.