To PDF a complete quark document into one PDF file, you essentially do nothing. There is a form field at the bottom of your PDF dialogue box asking what pages you would like to PDF... just leave this field blank and all pages will end up in one PDF document. Under that same field, there is a drop down menu where you can select different styles of PDF, just select the type of PDF you want. As for downloading from the Web, the answer is yes, you will need to upload a new whole PDF.
Tonya Morris | Designer
Meeker, Colorado