Hi Arron,
I use Arbortext Editor with styler to generate my PDF files and I use Adobe Illustrator to create and edit illustrations. The issue with eps is specific to my working condition, I get some eps from my japanese colleagues and it is really heavy and highly vectorised with a lot of layers. Because of that sometimes the Editor does not generate the eps illustration in my PDF.
My solution so far is to work with illustrator to create and edit eps before to export the eps to a tiff file. I handle two library of illustrations, one in eps and one in tiff.