And when you replace the oil in these things do you wait until is starts leaking out the overflow bolt (behind the gear shifter) or do you put what you think is the right amount and then run it for a while to check? I know this is what the manual says but I thought the other method would be a lot easier.
If you drain from both plugs, and service the filter, the bike will take one liter of oil exactly. That works every time, and there is no need to ever bother with the overfill plug. One quart without the filter.
Regarding the overfill plug, the manual does not say that you are to fill the oil until it comes out the bolt. That would cause you to short fill the oil by a huge amount. The manual tells you on page 3-9 that only if the oil shows above the high limit mark in the fill window do you then remove the overfill plug. The way it works is that there is no additional room in the oil "tank" for any additional oil, and anything extra gets routed back to the sump. The overfill plug then is set at the highest level oil should be after the engine has been run and all the normal amount of oil has been pumped out of the sump, leaving it "dry". If you were to fill only to that level, there would be almost nothing in the engine.
If the bore/rings were damaged wouldn't I see smoke coming out of it?
In order to burn 100cc of oil in an hour, there would need to be only one half microliter of oil (0.0005cc) in the cylinder each time it fires, figuring an average of 6000 RPM. That's not going to make a whole lot of smoke, but yes, there probably would be some.
Review your oil fill procedure again, then worry about it.