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