LILO is easy when you have two seperate drives. Put LINUX on the primary master and Windows on another drive located else where. Yes, windows can be located on a secondary controller but only if you installed drivers and you know the drivers are working properly. Then set your motherboard to boot to the primary master. This works for my computer when I installed Windows XP. I recently uninstall Windows XP because sound card drivers weren't yet supported and video card drivers keeps giving me infinite looping errors. Well sound card drivers were supported but I want 5.1 channels that Win98 gives me instead of two channels.
LILO goes on your master boot record. The LINUX how tos explains about how LILO works and its uses.
Windows XP is a combination of Windows 98 and Windows NT. You get the IRQ sharing feature and vast hardware support of Win98. Other features of Windows XP you get more security, good memory management, and good stablity of Windows NT or Windows 2000.
Don't forget Windows ME has Boot.ini too.