Most software I've used for DVD projects with menus have sucked in one way or another. Limited background audio, limited menu templates, etc., but you eventually end up with something "close enough" to what you want. It's not really difficult, just tedious to mess with and get things as you might imagine them, or "close enough." In other words, it sucks, but isn't really hard to do once you find something that works.

Two other things - some (most) video software loves to use its own codecs, and may or may not "respect" the imported video (or audio, especially with so many tracks...); it may re-render it in the process. You may or may not be able to bypass that, or put the 'original' back in place without some further tweaks (see this thread for an example: http://forum.doom9.org/archive/index.php/t-161144.html)

After it's done, the only way I can think of to keep it separate would be to create your own ISO from such a program, mount it, and then copy out from there. That way people can put it together on their own, or just have the main file.

A good list of such software http://www.videohelp.com/tools/sections/authoring-bd-hd-dvd