Unless the Bonnie's petcock/tank setup is very different from other types of bikes, there aren't separate "main" and "reserve" parts of the tank. On most bikes the "ON" position simply takes in fuel from higher in the tank, and when you switch to "RESERVE" you're allowing the petcock to take fuel from lower in the tank.
Pretty much the only reason you have the "ON" and "RESERVE" position is so you KNOW when you're running low on fuel before you run out. If you forget to turn your bike back to the "ON" position after filling your not going to "run out the reserve". If you leave it in the "RESERVE" position however, your not going to know when you're running low. If you're in the habit of turning your petcock to "OFF" when parking this won't be a problem unless you put on 140-150+ miles straight (running through an entire tankful).
Turning the petcock to the "OFF" position when parking is a good practice because it can save your butt if you have a leaky fuel system or one of flooding due to a stuck or improperly adjusted floats - though my (and others', from what I've read) stock petcock seems to leek like a sieve anyway. I can run the float bowls dry and if I leave her for a day with the petcock "OFF" she'll still start right up.
Some bikes have also been known to have inconsistencies in the distance between the two holes or length of the tube. This could be part of the reason why some are hitting reserve so much earlier/later than others. When I last hit reserve my bike took 2.9 gallons of fuel, for example, four miles down the road (negligible) - meaning if Triumph's quoted fuel capacity is correct, I still had 1.5 gallons of fuel in my tank (just over 1/3 of a tank) after hitting reserve.
Regarding "old fuel" being left in a tank - if you put "new fuel" in on top of "old fuel" after the first few "sloshes" you're going to just have a tank full of "slightly less than new fuel".
This is of course assuming I'm right about the Bonnie tank being a single reservoir tank.
