The "common wisdom" has always been to use HDs as masters and CD-ROM drives as slaves, unless you only had one HD, in which case you'd use both the HD and the CD as masters.

So in your case, you'd use the CD as a slave in whatever IDE channel you want. It doesn't matter which.

Just answered on your other thread but will do it here for completeness in a slightly different way
Basically you don't want drives that you'll be using at the same time on the same IDE channel as they will have to wait for each other for the IDE cable to become free.

This is to squeeze every little bit of performance out of the system. I've come across many systems that had both on the primary channel and nothing on the secondary and were fine
The CF card with the almost instant seek time and constant read/write speed will also hide any delay that you would have had with a traditional HDD anyway.

so short answer go with whatever works!

Great! thanks!
I am using a CF and real CD-ROM on Primary (Win98SE on this one)
and
another CF (standlone) on Seconday (planning to install games on this one only)