I do work for offset printing almost daily and I'm pretty familiar with that problem. You can't set overtprints/knockouts directly from Inkscape, but that probably isn't a big issue, since there is a bigger problem: what format to use when sending that file to the printshop. I wouldn't send an SVG file to a printshop. It's probably a recipe for disaster (although they probably won't accept the file in the first place). You should be sending PDF or TIFF files. Inkscape's PDF output isn't very reliable for print work yet, so you have two options: - Export a high resolution bitmap and export it as TIFF using GIMP - Import the artwork in Scribus and prepare it for print, then export as PDF.
You have to keep in mind a couple of things, though: - Scribus SVG import doesn't play well with text, transparency and gradients. And forget about masking and embedded bitmaps. Use Scribus only for plain vector artwork or text converted to curves. The pro about it is that you're keeping vectors, and that's good specially for text. - Creating a TIFF for print from Inkscape and GIMP involves some steps and may look complicated, but it's a reliable method with less chances of screwing it. For two ink works like yours, you can use an old trick: replacing the CMYK plates for spot colors you can create up to 4 inks artwork. So, create your artwork in Inkscape, use spot inks (you can convert any color to spot swatch using the fill dialog). Once you're done and you like the result, edit your two inks and change the to pure RGB magenta (#ffff00) and cyan (#00ffff). Export the result as 600 dpi. Take the result to GIMP, decompose to CMY channels, invert, and save that channels individually as separated files (one for each plate) or paste those plates into a CMYK separation created with Separate+. If you need to overprint the top layer, just export the two plates separated from Inkscape and put them together in GIMP.
I know this will sound complicated and tedious, but once you made it a couple of times makes a lot of sense and gives you total control over your separations, and it's relatively fast to compose the file For example, this is a duotone (just two inks) using that method: http://dl.dropbox.com/u/255376/print-tests/Duotone-Print.JPG :-)
You can automate most of these procedures using imagemagick, but probably it's a good idea to start doing it visually so you can understand the process and come up with a proper command line version easier.