The application manager is configured to automatically run 'apt-get clean' when finished, so nothing is left over in /var/cache/apt/archives.

In any case: 'Manual' installation of .debs to avoid possible future unavailabilities of repos won't save you work, it'll instead just create lots of extra work in your day-to-day package managment, instead of the very rare once-off repo unavailability. Also, it doesn't matter which repo a package comes from, so if a package A depends on package B then package B can come from any old repo.

And lastly, if you simply just want to store any installed package locally then you can use apt-get install to install the packages, and avoid running apt-get clean ever. Unless configured to do otherwise, this will leave every installed package in /var/apt/cache/archives/, from where you could also copy to somewhere else for long-time storage. (Or just try to find the config the previous poster mentioned, if so you could continue to use the application manager.)