Yeah, I think you're definately gonna need IDEfix for the 2nd channel. It's probably best to do a full install, but I have got away with just putting the file IDEfix in the C drawer of Workbench and adding 3 lines to the Startup-Sequence of an A1200 Tower recently.
If Exists C:IDEfix
C:IDEfix
EndIf
OS3.9 does ask that question. If your CDrom is working when you create the Emergency-Disk the files should be copied over to it from Workbench. But it doesn't always get it right in my experience and a bit of driver adjustment can be required.