Yes, smb.conf is written at boottime. You can cheat by renaming nmbd and smbd to nmbd.orig and smbd.orig and then create shellscripts named nmbd and smbd which start nmbd.orig and smbd.orig using your own smb.conf (nmbd -s path/to/your/smb.conf -D, same for smbd)
JockyW
PS: If you can give recommendations for smb.conf please post them here