Using multiply effect on illustrator file with 2 color job?

Hi,
Encountering a tricky problem and not sure if its an InDesign fix or an Illustrator fix.
I am working on a 2 color job—pms color + black on a book cover. The cover needs to seperate into these 2 colors.
Also, I need to make a high res and lowres pdf that look like the cover to send out to marketing, sales etc.
WHAT's THE PROBLEM?...
Well, I am creating a collage with black ink vector graphics on top of the pms background. I created this art in illustrator. it is saved as an .eps file. The illos were done by someone who used a white fill to knock out black areas. There is also a wide 50% grey outline around the illustration.
I like the idea of the line of the illo being black and the fill being red so that it looks seethrough on the red background. But the 50% grey outline causes a problem...I'd like the 50% outline to blend with the red color, so instead of appearing like there is white in the ink it overprints.
The only way I could think of (and quickest way) was to apply the multiply filter in illustrator to the vector illo. This seemed to work great.
I brought the illo into InDesign where I created my cover layout.
Looks great, Prints great. Separations appear to be good, although it shows the yellow, cyan, and majenta layer they appear to be blank, so I think it will seperate nicely into 2 plates–PMS + black.
BUT, when I make a pdf, using "smallest file size" or using "high quality print", the pdf it makes does not show the illustrations in the collage. They are kind of beige and dulled out. The publisher needs pdfs too.
Does this at all indicate that this job will not print correctly using this multiply filter, or is it all well and good final product wise, but its just an issue making the pdf? I am slightly nervous I am going to send this off to the printer and they will have some issue.
I am a professional designer of 10 years with lots of print experience, but I have never used multiply in illustrator so I just want to make sure there is no rule against doing this I should know about. Does multiply at all mess with the color separations or is it fine? And how do I get my pdf to come out right? I'm hoping there's some dumb thing I'm forgetting, or a simple fix.
Thanks for any insight you may have!
L.

I did figure out after posting this that I was using one .ai file and one .eps file—the .ai was showing up fine in the pdf and the eps was showing up screwy.
odd thing though, when I just re-exported using pdf/x–1a settings, now both images appear muddy! but fine when I turn "overprint preview" on. I just don't want my publisher to have to tell everybody to turn overprint preview on...they shouldn't have to do that for editors etc, non design people.
maybe the new "smallest file size" will be fine though since this is a press preset...we'll see.

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