Some packages in the Software Center may be free but are offered under a proprietary license. For this reason (the license) they are not included by default in the Ubuntu apt repositories.

When you install one of these packages via the Software Center it will create a new apt source file in /etc/apt/sources.list.d/. In the case of Master PDF Editor it will create:

private-ppa.launchpad.net_commercial-ppa-uploaders_master-pdf-editor_ubuntu.list

Once that file has been placed in /etc/apt/sources.list.d/ you can then use the regular apt/aptitude commands to update it.

I also want to add that sources like this often require authentication. If they do a comment will be placed in the source file indicating as such:

$ cat private-ppa.launchpad.net_commercial-ppa-uploaders_master-pdf-editor_ubuntu.list 

deb https://private-ppa.launchpad.net/commercial-ppa-uploaders/master-pdf-editor/ubuntu precise main #Added by software-center; credentials stored in /etc/apt/auth.conf

At the end you can see the comment, "credentials stored in /etc/apt/auth.conf". That file will store a hash of your password like so:

$ sudo cat /etc/apt/auth.conf # Needs root to read the file

machine private-ppa.launchpad.net/commercial-ppa-uploaders/master-pdf-editor/ubuntu

login riskable

password someGobbldyGookHash