Define crap and explain where they look like crap on screen, proof, or your inkjet/laser printer?
Postscript printer or a comercial grade inkjet?
You might saving down to version 8 eps files in illustrator, We always have problems with version 9+ eps files in Quark 5.
When bring images from Illustrator file to Quark us EPS format, and do as your print advised rasterize and flatten any transparence effects. Not the who document mind you. Simply the element interacting with the transparency effect. Ideally you should do some testing to see what works best with your own or printers workflow to see if there RIP, software, and equipment can handle the transparency.
EPS are strange beasts. The were primarly designed to be embed directly into the print stream to a postscript printer. Most software will not display the actuall EPS file, as it would require the software to contain an postscript interpreter. The full image is also lot of data to push around since many documents my contain 400+ megs of 300dpi images.
So most publishing applications like Quark, Indesign, Pagemaker, etc use a low res proxy on screen. Quark is such a program infact you can't embed images in a Quark document, they are all linked to high-res'es on disk.
So what you are seeing on screen In Quark is just a low res proxy, Quark either generates that proxy or makes use of the preview embeded in the EPS. Quark 6 I think allow a better quality proxy but for the most part it's just that a proxy.
Unless it has change since Quark 4, that same proxy is also what's sent to non-postscript printers (ie. Inkjets and cheaper laser printers) Non-postscript printer can't parse an embeded EPS. This would again require a Postscript interpreter.
I would try generating a PDF to see if the image are actually effected.
J. Stuart J.