erm, i'm definitely confused as to what your problem is.
the .cue and accompanying .bin files are one of several ways to store images of CD's, just like .iso's.
Among other tools, Nero can play with .cue files.
My personal experience shows that for some reason (better organization, perhaps, or maybe even some compression), .iso is more compact, so it's recommended to use .iso instead of .cue/.bin if you have a choice.

A tool that can convert from bin to iso and back is WinIso.

If you want an easy interface w/out having to worry about the how's and why's, just use Nero. It can also play with both formats (.bin and .iso), and you won't have to understand the underlying details.

Here's a starting point, however: digital-digest

hope this helps