Thats good for sticking flat surfaces but if you put it on the screw it could set with the screw not holding the strip down enough. The matchstick method works in most cases and can't make the situation any worse.
I'm certain that you can get floor trim designed to "link" carpet and tiles/other hard floor coverings... the two undersides of the strip are different.
Use the screws that are provided with the carpet strip. They're specially for this purpose as they have a domed head that fits flush with the strip. By all means use different screws or nails, but you'll probably end up with gashed feet or knees.
I had a similar problem chrissa, I wellied it with a hammer and it flattened out and didn't get in the way. Getting it out again will be almost impossible though.