At first, select PDF file to encrypt. Then input user password and/or owner password
( N.B. Password should not contain quotes.
If your version is less than 0.1.9, it also should not contain spaces ).
Then select encryption method and features that will be allowed/forbidden.
Features to be allowed should be checked, features to be forbidden should be unchecked.
For more information, please see pdftk help.
From version 0.1.6-1 you can overwrite input file with encrypted one.
To do so, select 'No' when asked whether you want to create new file.