...if you can't select separations in your print settings, then your printer driver doesn't support host based separations, so you will have to use a work around...
...with regards to aliasing colors, you can't map process colors to spot colors, it has to be spot to spot or spot to process, otherwise the alias function will not be available...
...without seeing your artwork and what links are causing the problem it can be difficult to problem solve, but from experience aliasing colors in indesign can work, but not always. In reality it is safer to fix the source artwork in many cases and in the long run...
...as for printing separations, your next best option is to either simply proof onscreen using indesign (or from a composite PDF in acrobat pro and view separations)...
..to physically print separations without a driver that supports host based separations, you can use the "postscript file" option under "printer" in the print dialog and using a PPD that supports custom page sizes and host based separations...
...then in the output options you can use separations > click save > locate the postscript file created > distill with acrobat distiller (or open the postscript file directly in acrobat, the PDF creation settings are control in Acrobat Pro's preferences, under "Convert to PDF"), then print from acrobat all the pages (which will all be in black)...
...you can also use the Adobe PDF printer driver to create a PDF with separations, which is installed along with Acrobat Pro, this allows direct printing through Distiller and creating a PDF on the fly (although with Mac OS X Snow Leopard, this has now changed and can't be done without saving to postscript file first, then distilling)...
...if you don't have a PPD that supports separations, then you can download mine from below, used for an Agfa Apogee X system we used to have. What PPD you use is not overly important, it just has to allow separations and custom page sizes essentially, to allow you to get a postscript file:
andrew