If you do this in a code node:
ods pdf file='all_in_one.pdf';
** proc or analysis 1; run;
** proc or analysis 2; run;
** proc or analysis 3; run;
ods pdf close;
You will get the results of all 3 procedures in one PDF file. I suspect that EG is isolating each task within a separate ODS PDF "sandwich" and so, if you had 3 procedures or tasks, you would get 3 separate PDF files.
If you do not use the above technique (putting all your procedure code within one ODS PDF "sandwich" in a code node, then you would need to use an Adobe product (Adobe Acrobat, PageMaker, FrameMaker, etc) or some third-party PDF builder in order to concatenate multiple PDF files together into one file.
The good news is that EG will let you export the code from your project and then you can grab that code and insert it into one ODS PDF sandwich,instead of the way that EG is doing it now.
I agree with Cynthia's solution of sandwiching the procs in one "ods pdf" code note. Also, for my particular situation I still needed a third-party PDF builder to combine various PDFs using my BY variable. I used something called PDF Split-Merge with had both GUI and command line support so I can process it in a batch file. It was also very inexpensive. http://www.verypdf.com/pdfpg/index.html