At first, you will have to select PDF file you want to attach files to. PdfTk-QGUI will try to get necessary information about this file (number of pages, encrypted/decrypted). If selected file is encrypted, you will be prompted to enter a password. If you enter correct password, PdfTk-QGUI will decrypt this file and work with decrypted copy.
You can add/remove files in the list using the corresponding buttons.
For each file you can specify page it will be attached to (default - first page).
From version 0.1.6-1 you can overwrite input file with a new one.
To do so, select 'No' when asked whether you want to create new file.