No, I don't think it will make any difference.
Bear in mind though that to set up the dual boot LILO will replace the MBR for the dual boot. It won't screw up windows, but it could be difficult to remove LILO if you ever wanted to. ie you will not be able to get rid of the choice of OS screen.
I did get rid of it from a win2k installation just by booting from the win2k cd and choosing R and then C (console) and writing a new MBR.
Nick