Yeah, you should edit your bootmanager config files. For an editor, I like mcedit which comes with Midnight Commander package. Vi is a good choice too.
You should copy the old entries in lilo.conf and rename them for the new kernel. Like this, label="something you had before" becomes label="NForce-AGPGART kernel" for example. Also remember to change the image parameter.
BTW: running make install after make modules_install should fix the lilo bootparameters for you.
What comes to X, has it stopped from starting after you compiled a new kernel? it would help if you could post the contents of file [b]/var/log/XFree86.0.log