Okay, there are two ways to make cue files, both are very similar.
The first way is for when you rip an entire album into one file (for gapless playback, for instance). If you do it with EAC, there's a menu option to generate one automagically with the right data inside. You can also do it manually, which is done just like the second method except with a couple slight differences.
The second way is to do it manually. Create a file that looks like the following:
CODE
TITLE "Album Title"
PERFORMER "Album Artist"
FILE "C:\Path\To\File01.mp3" WAVE
TITLE "Track Name"
PERFORMER "Track Artist"
TRACK 01 AUDIO
INDEX 01 00:00:00
FILE "C:\Path\To\File02.mp3" WAVE
TITLE "Track Name"
PERFORMER "Track Artist"
TRACK 02 AUDIO
INDEX 01 00:00:00
and so on. You can indent lines however you want.
You can also add a line "INDEX 00 min:sec:ms" before the "INDEX 01" line if there is a pre-gap, you can add it before the "FILE ..." line if it's at the end of the last file.
One thing I added is to interpret a line "INDEX 02 ..." as the *end* of that track. Add that after the "INDEX 01" line.
Finally, there can be more than one track from a single file. To do that, just change "INDEX 01 00:00:00" to show the time at which that track starts within the last file mentioned. And of course, leave out the "FILE" line.
Hope that helps. One last thing: you can use any file format that foobar can play. You should even be able to use streams (although I haven't the slightest idea how that would work) or the tone generator.