First, I don't have a Z4000 (or it's side remote), I use the Lionel PH-180 bricks for all train running and I have command only, no conventional, so not a lot of experience there.
However, I did try conventional once using the method Lou1985 describes with a variable channel using the thumbwheel to control the conventional train. It worked well, but it was only to briefly test out an old train set my daughter had from 1982. As soon as we saw that the train worked for a few laps, I put the track feeds back to the fixed channels and put the conventional train back in storage. As I recall I used Barry's book to make the changes. That was about 5 years ago.
IMO, I think the easiest way for you to run your conventional engines is the way Paul 2 describes above using the fixed TIU channels and the Z4000 handles. Use the handles to control conventional trains. Then set the handles to 18 volts when you go back to command operation. That should get you up and running fairly quickly. You could at least run your trains until you can sort through the other stuff and get it all up and running the way you would like.
The 2nd easiest method would be the way Lou1985 describes using the variable channels set to fixed so you can run your command control stuff and using the thumbwheel to control track voltage only for conventional operation. Not a lot more difficult, but that are a few more steps and settings to deal with.