Speaking purely from an engineers perspective you actually do have to pay a bit of attention to running the engine in.
When you first get the bike, the whole engine is "tight". This means that nothing has been worn in at all. The piston rings are very tight in the bore, the bearings have not been run in at all, the valve springs are going to be very tight etc etc. The big thing with this, is that the engine is not designed to run hard when it is so tight. Thats where the running in period comes in. There is no real way to know if the engine is properly bedded in or not, its just a common sense thing. Don't get on and flog the jesus out of it on the first ride coz you could possibly score the barrel or do other nasty stuff.
In my opinion (and i've never actually broken in a brand new engine, only ones that i've rebuilt) i'd take it quite easy for the first ride of about 20 mins. Just cycle through the gears at quite low revs, but don't really punch it, just cruise around as if you were taking your grandma for a spin on the back. After the first 20 min ride, take a break for a while.
On the second ride, you can go a little harder, but still, the engine is going to be tight, so just work into it slowly but you can give it a bit more.
With each ride up until you've got maybe 1.5 - 2hrs under the belt, just slowly get harder and harder. After this said time, change the oil and you should be right to ride your life away!!
The other thing that people don't think about when they talk about breaking in a bike engine is the gearbox! Gears need to be properly seated and have a bit of use before you should really go flogging them. Gears will wear uniformly over time so you have to create some wear marks on them before they will really work well. Same with bearings, they should really be run in a bit before giving them a flogging.
Of course, its up to you how you run your bike in, there is no "biblical" way to do it, but just use a bit of common sense and i'm sure you'll be fine.
Cheers mate.
Matty