Thanks for post. I’m afraid that I’m not quite sure what you mean. For Help & Manual 4, you should be able to specify a full path for the Project File (on the project tab) and a different full path for the output PDF file (on the PDF Options tab.)
What version of Help & Manual are you using?
Finally, if nothing else works than can you use a Move File(s) action to move the PDF files to the correct output folder (although this should not be necessary.)
I'm afraid I'm still a little confused about what you need to do. How many actions are you using?
If you're using a separate Help & Manual action for each project, then you should be able to set each one up with a path for the project, and the path for the output file.
If you're using a File Iterator to select each project, you'll need to be a bit tricky.
Say if you have a variable called HMProject which is set to the full path of the project file.
Create a second variable called HMName. Then add two Path Manipulation actions. Set the first one like this:
Input -> From Variable -> HMProject
Output -> Specify Output Variable -> HMName
Path Functions -> Extract File Name
... and then set up the second one as follows:
Input -> From Variable -> HMName
Output -> Apply to Existing Value
Path Functions -> Change File Extension -> .PDF
... then you can just set up the H&M action to build project %HMProject% to output PDF file \Help\PDFs\%HMName%
This is getting pretty complex, so please just let me know if you'd like me to mock up a demo project for you, or if I've misjudged your requirements entirely.