Ah, the problem is that DVD Workshop will not allow you to hear AC-3 (Dolby Digital) audio, which is the format in which the E-50 records. To get that capability, they want you to buy the more expensive version that DOES support AC-3 (actually it's not that much more right now -- I think they want $299 for it).
However, what you get in that version really is the ability to CREATE an AC-3 audio track -- you don't really need that since you already have an AC-3 track on the files from the E-50. All you want to do is LISTEN to what's there, but unfortunately they've taken that capability away. A while back, there was a "hack" posted here that allowed you to change a setting in the .INI file to turn the AC-3 "listening" on, but that option is no longer available in the current non-AC-3 version.
In short, you're not doing anything wrong. That's just the way the program works, unless you buy the AC-3 version.
P.S. I guess I should point out that your AC-3 audio WILL pass through to your finished DVD that you create in DVD Workshop, as long as you use the "do not convert compliant file" option.