The reserve gas is not in separate gas tank. Just below where the normal gas exit hole is. You do not need to run into your reserve any more than you need to run your car to empty (that is, you should never need to). Pictures and added details here: http://faq.ninja250.org/wiki/How_does_the_reserve_tank_work%3F
Actually, I just read something here ( http://faq.ninja250.org/wiki/How_far_can_I_go_after_putting_the_fuel_petcock_on_%22reserve%22 ) that says you should run it into reserve every once in awhile… I’m not entirely sure about this personally… I prefer NOT putting dirt and water through my carbs… I’ll need to read up on it some more…
When you are filling up your tank you set the gas to OFF if your bike has it, or simply ON in the case of an auto-off petcock (My ZZR-250 only has ON and RESERVE. It automatically sets the petcock to OFF when I turn off the engine. I don’t know if that is the case with the Ninjas).
You do not fill your bike with the setting at RESERVE for one simple reason, if you pull away and forget to set it to ON, then you have no warning for when you are low on gas. Instead of sputtering out and switching to reserve, you’ll sputter out with no more gas to get you home!
Best way to know when to fill up:
Zero your trip odometer every time you fill up. That way you’ll know how long you’ve been running on that tank of gas. Fill up the first few times about 150 miles. I think the Ninja 250 gets between 200 and 250 miles to a tank. After you’ve done it a few times, you’ll know how much gas it takes to go 150 miles for you. Then, compare that amount of gas with your tank size (4 gallons I).
Me, I fill up ever 300 Kilometers (being metric and all) and that usually has me filling up 3/4 of the tank. This is a good habit for me, since I know that as I near 300km I should start looking for a gas station, but I’m not so near empty that I have to fill up at the first one I see.
First Days Living with your new-to-you Ninja 250