Jeff,
The complete answer requires a lot better typing skills than I have, 'cause its long. I'll refer you to Precision Shooting magazine, they have had most of the info I use.
To make it short, basically, the two schools of thought are: 1) Use non-moly'd bullets, they will help remove the microscopic burrs in a new barrel better; and 2) Break it in with what you plan to shoot, those are less burrs than microscopic scratches, better to fill them with moly than gilding metal.
Break-in, generally, is a process of starting with a clean barrel, and keeping it clean for the first series of shots. Almost invariably, a custom barrel will show signs of being broken in in a very few shots (10-20), while a factory bore will need many more. This is almost certainly due to the custom having been handlapped, and given greater attention.
"Just shooting" the rifle means, to me, that you will put one layer of fouling on top of another...
Finally, the rifles that I've broken in properly are much easier to clean than the others. And don't lose sight of the fact that this technique was developed by shooters to whom a 1MOA group is not a triumph, but a disaster!{;0))