So as best as I can tell, you have several "mixed" CDs, on which the music plays continuously across the track markers. When ripping these CDs with CDex, they are broken up into the component tracks, but you want to keep them as one long track. So that means you need an audio editing program.
I use Soundforge 6.0 for all of my audio editing. Granted, this program is probably overfeatured and very pricy for what you want to do; I procured it through my company.