How does update work with programs installed from .deb file

This is indeed kind of complicated. First, apt is a front-end to dkpg which actually handles installing/removing packages. So, /etc/apt/sources.list (and any files in /etc/apt/sources.list.d/) are read by apt, not dpkg.

Now, when you download a .deb file manually, you are bypassing apt and will use dpkg -i packagename.deb to install it instead. This means that apt's database will not be updated and that the apt system will have no knowledge of the package you installed. In other words, apt-get upgrade will never update any manually installed packages.

Having said that, chrome is actually an exception to the rule. When you go to its download page, you will see this message:

 

At the bottom is this note:

Note: Installing Google Chrome will add the Google repository so your system will automatically keep Google Chrome up to date. If you don’t want Google's repository, do “sudo touch /etc/default/google-chrome” before installing the package.

This means that the .deb package includes a script that will add Google's repository to your system (specifically, it will create a file at /etc/apt/sources.list.d/) thereby ensuring that chrome will be updated when you use apt-get.