You turn off the override in the Fiery, or set the screen there.
I can't believe Xerox passed the buck on this. If they can't instruct you in how to do this over the phone, it ought to be in the documentation they should have provided with the equipment. Been awhile since I worked at a service bureau, but when we got our first Xerox color copier they sent a person to our site to set it up on the network and train us in how to use it, and they gave us a number to call when we needed help.
Thanks for your response Spier. The problem seems to be that nobody has the complete picture; Xerox support doesn't really know that much about command workstation (even though they're responsible for giving it to you), and this doesn't seem to be an InDesign issue. I ended up talking to a guy at EFI and he told me that to control halftone density specifically, you need the Command workstation Graphic Arts Package (sold through Xerox apparently). With that add-on to Command Workstation you can do what they call "halftone simulation," which allows you to specify screen densities for a job. The package retails for about $7000 on the EFI website, but we'll see what the Xerox rep says. Just thought i'd leave my breadcrumbs here for anyone else who might run into the same issue and comes to the Adobe forum.