When I click on a pdf it automatically downloads and the download manager pops up but no program opens. I downloaded FoxIt for pdfs but still same problem.
First, make sure that you have the latest version of WaterFox by going to the Waterfox button -> Help -> About.
Now, follow this:
For step 4***, you can select the Foxit Reader plugin if you want to view the file inside your browser.
NOTE: Mozilla are currently working on a PDF.js reader that automatically converts the PDF file to open web language. This is a work in progress, but it is more secure and faster than using another separate program, but you might have some issues with some PDF files. If you are interested, see here for the PDF.js extension.