startup disk utility

I have been fixing my permissions by just using the disk utility in the app. folder. I don't remember if this is the way you should do it or to get a good clean should I use the startup disk and hold down the c key. I used to do that yrs. ago. If you should do that I only have the origanal panther disk, 10.3. I since have 10.4.11, but no Tiger disk. Can I use the panther disk to use that utility or is using disk utility all I need to worry about ?? I'm so curious if I have been doing it wrong all this time.
Thanks for any help.