I am using Desktop Version, Clicking on Toolbox, and then Protect PDF.
I add my file, and type the password into the box.
I click on Protect PDF files, then Save.
I can open the PDF with the password, but if I want to make any changes, it asks for a Permissions Password. I have tried the password that I put to open the PDF, but that does not work.
the tool Protect PDF sets two passwords: the User password to open the PDF and the Owner password for the permissions. In older versions, if only the User password was entered, a random owner password was set that nobody knew. That is why your open password is not accepted as permissions password.
Since version 11.31.0 the open password is also used as owner password if you leave Owner password empty. So:
Protect your original, unprotected file again with Protect PDF.
If you want a separate permissions password, enter it in the field Owner password (if you only see the password field, click the cog icon next to it). With the checkboxes you choose what is allowed without this password, e.g. Printing or Modification of content.
With this password you can then change the permissions in your PDF program.