the answer is yes, this program wont 'undo' any thing you've setup, it will just work on top of it during the time you specify (like each time you turn your phone off, it will come on the next time you turn the phone back on) or you can even have it come on as soon as the backlight dims. You can set it to your preferences. Give it a try and let us know if you have any questions.
There's a new updated version that just came out yesterday:
http://www.freewareppc.com/utilities/s2u2.shtml