User Password and Owner Password are 2 different types of security which can be set depending how secured you want the PDF, you can reference below for information on what User vs Owner does:
User Password- The user password, if set, is what you need to provide to open a PDF. The PDF reader will prompt a user to enter the user password. If it's not correct, the document will not open.
Owner Password- The owner password, if set, controls permissions, such as printing, editing, extracting, commenting, etc. The PDF reader will disallow these things based on the permission settings. The PDF editor will require this password if you want to set/change permissions.
The Toolkit method EncryptPDF encrypts an unencrypted PDF file to the specified encryption level, sets user and owner passwords, selects permissions for how the PDF may be used.
pRetVal = object.EncryptPDF(nEncrLevel, InputFileName, OutputFileName, UserPassword, OwnerPassword, CanPrint, CanEdit, CanCopy, CanModify, CanFillInFormFields, CanMakeAccessible, CanAssemble, CanReproduce);
See also SetPDFSecurity