ok, last time i answered a question about this i got it wrong ... let me see if i can find the link ... here we go :
http://www.linuxquestions.org/questi...669#post381669
I have as yet, never had an issue with System map, even when i go back to an older kernel. The bigger issue i've seen when doing this is that the modules are screwed up. But what i generally do is copy the new System.map file to the /boot directory and append the filename with the same string as the vmlinuz file/
As for the defining a separate System map via lilo ... no idea. (edit -> not necessary - check the last link).
for a bit of a gander ... do a
less /boot/System.map
(while root)
sorta interesting really, it looks like it starts with crc signatures, and moves on to addresses ...
For indepth stuff (including a detailed explanation of what System.map is) check out
http://www.dirac.org/linux/systemmap.html/