Adobe InDesign & Quark Xpress: yes, we do recommend using the "export to PDF" feature and choosing the PDF/X-1a:2001 or PDF/X-3:2002setting when doing so. It is important to use this PDF setting to ensure you have a stable PDF for printing.
All other applications: we recommend either: (1) print directly to PDF using PDF/X-1a:2001 or PDF/X-3:2002, or (2) print to PostScript file, then distill to PDF using PDF/x-1a:2001 or PDF/X-3:2002.
Before creating a PDF in any of the above options, we recommend converting all custom/spot colors (even those with transparencies) to CMYK.
The above recommendations should allow you to produce a solid and stable PDF that is ready to print.