I use both Quark & InDesign and think that Quark will never ever catch up to the versatility and ease of use that InDesign has incorporated into the program.
The first thing you should do is contact your printer & see what versions he has & how he prefers to receive your files.
The printer I use prefers pdfs but will take all major programs as well. He supplied me with the ppd for the profile he uses and I downloaded Creo Assistant to make everything work properly with his equipment. One of the magazines I build can print either as cmyk, as black plus a spot colour, or as cmyk plus a spot colour (depends on the advertising). I make the pdf selecting the Creo driver and the supplied ppd and the 5 colours show up perfectly. He made sure I sent him a sample so that he could test it before I got too far into the production process.
When the magazine starts getting too large, I make a pdf for the front half and another for the back and join them together in Acrobat. This seems to speed things up a bit.
The preflight that is built into InDesign has caught all manner of problems arising from supplied files (rgb, wrong dpi, missing fonts in eps files, etc) and this has solved all my problems long before they got to the printer.
I also give the printer the native ID files just in case he needs to go in & make a change at the blueline stage.
I have worked with both programs since their first release but I now use Quark only when I absolutely have to (supplied files or a printer who does not take InDesign). We are finding that the percentage of jobs being supplied to us in InDesign has now far surpassed those supplied in Quark.
