Adobe should make the "Use a certificate" method in Reader be a two-part process:
The first part allows the user to place the signature graphic and adjust it until it's just right
The second part should be the "Sign" button that actually locks the the graphic in place and digitally signs the file, opening the save file prompt.

The problem:
It's difficult to know if you have drawn the correct sized and shaped box that the signature graphic will appear in. You are only able to know if you did it correctly AFTER you have signed the document digitally, and saved the PDF. If you made a mistake in the placing of the graphic, then you have to reopen the original PDF and start the "Use a certificate" process all over again and save the document the second time.
If the user had a chance to adjust and tweak the location and size of the graphic before "signing" the document, they would be sure that they are happy with how it looks before the PDF is cryptographically signed.