Having both OS 9 and OS X on the same volume should not be a problem unless you go rummaging around the OS X system in OS 9. OS X has many mechanisms to protect itself from inadvertent damage, none of which are recognized by OS 9.
Two disks came with Mac...both are version 9.0.4.
One disk says Software Install the other Software Restore
Please excuse my confusion. From your previous posts you apparently do have a set of OS X 10.3 Install CDs. I rashly assumed those came with your Mac. In any case follow my instructions using the OS X 10.3 install disc 1 that you have. It will work the same way.