You don't need a new application to do what you are asking–if I understood correctly. you can still use a word processor to create the document (I assume you are using Microsoft Word, since you mention you created the PDF file through the "Save to…" command), and then use Preview.
Here's how you can do it:
After you create the document in Word, go to the "File" menu in Word and select "Print". Then, at the bottom of the Print panel select "PDF" and then "Save as PDF". It's probably best that you select your desktop to save it for now (in the "Where" field).
As you said, this will create 2 or more PDF files because you used section breaks in Word to change the orientation of some pages within the document. Let's say your original document is 8 pages long and you have changed the orientation of pages 4 and 8 to landscape; that means you'll end up with 4 separate PDF files: the first one containing pages 1, 2, 3, the second PDF file with page 4, the third one with pages 5 & 6, and the last one with page 8.
Now use Preview to open the first PDF file that you generated (the one with pages 1-3 in this example). make sure you can see the page thumbnails in the sidebar in Preview. Now, select the next PDF file (page 4) and drag it into the sidebar hovering over the thumbnails of the first 3 pages - don't let go. You'll notice that Preview highlights all 3 thumbnails showing you that they are all part of the same file. Now, move this 2nd PDF file down to the end of the highlighted section in the sidebar, right below the thumbnail of page 3 (since you want to add page 4); a horizontal bar shows you where new file will go when you drop it in. Make sure you drop it WITHIN the highlighted region, not outside, since you want it to be part of the same file.
Continue in the same way with the third PDF file (pages 5, 6, 7) and then the fourth PDF file (page 8), making sure you drop them within the highlighted region and right below the last thumbnail each time.
After you've dropped them all in, select "File" in Preview, then "Save As". Here you can reduce the file size (Quartz filter) and/or password-protect your new PDF (Encrypt). Now you have a single PDF file that retains the different page orientations.
I hope that's what you want to do with your file.
Cheers!
PS: By the way, the Print panel in Mac OS X is the standard way to create PDF files on Mac OS X from any application that can print.
If this is not really what you want to do, and you still need a PDF editor, you can take a look at these two applications:
PDFPen Pro
PDFpenPro: Advanced PDF Editing Software for Mac OS X
or PDF Clerk
Mac PDF Editor | PDF Manipulation for Mac OS X