IDEfix does like everything. It is the most compatible software I ever saw. You may even remove the master and run the slave alone, which is forbidden in IDE specs. And of course having multiple partitions on multiple hdds is normal operation.
There must be something wrong with your setup. Do you have the latest version of IDEfix ? Did you check the cables ?
Does the Workbench partition work again if you remove IDEfix ?
Did you try hdd + cd-rom without the IDEfix software ?
Did you try hdd without cd-rom but with the IDEfix software ?
Did you check the IDEfix prefs program ? Perhaps your 4-way adapter is not recognized properly. Change the setting from Auto to your type of adapter.
Just for driving the cd-rom drive, you don't need the IDEfix software. Remove the section from startup-sequence. You only need atapi.device and CacheCDFS for running the cd-rom drive.
Bye,
Thomas