I like to use the aerobars to change my position while riding. It is a little easier for me to be in the aero, I'm more relaxed in the upper body. Also having another option allows me to not put so much stress on my body due to one position.

Have you been properly fitted on your bike? If not, you may also want to go down to a tri or bike shop and get fitted. If you're current setup is too long for you (stretching you too far forward) that may being putting unnecessary stress on your shoulders and neck.