you would only need to run PDFXEdit.exe /fileassoc:user=no
once but with Administrative rights - that will put the HKLM entry in place for new and unconfigured users.
Run PDFXEdit.exe /fileassoc:user=yes
once as the user on login to set them explicitly in HKCU.
Whether you do the per user for all your users or not is up to you, it may be easier than trying to determine who is already configured and who is not. Don't miss the former as it sets things up for new users down the road so they should not need to set it themselves (unless another association is set of course.)
Regards the Viewer, we did have something similar though I have not tested this in anything for years...
makes full association:
PDFXCview.exe /makeassoc:web=true // makes associations for both web and PDF files
for removing association:
PDFXCview.exe /makeassoc:web=false // disables plugins and makes association for PDF-files
PDFXCview.exe /makeassoc:web=false&webonly=yes // disables plugins only, association for PDF-files not be changed
I hope that helps.