Initially I used dpkg-repack but that won't include manpages for instance for all the installed debs. I also made a simple script to do all that as well but I found out red pill mode gives an option for one to disable cleaning apt cache which would leave all the downloaded debs in /home/user/MyDocs/.apt-archive-cache/ as per wiki states.

Though using this would only be effective for HAM (Hildon Application Manager), which meant that if say for example you used apt-get or FAM (Faster Application Manager) those deb files for instance would be saved in /var/cache/apt/archives.

Needless to say is that you can optify /var/cache/apt but for making /home/user/MyDocs/.apt-archive-cache the only place for downloaded debs to go you will need to add a line into your /etc/apt/apt.conf.d/00maemo:
This of course will not work in cases like using aptitude download where it will just download the deb file into your pwd (present working directory).

As for installing debs and its dependencies automatically, dpkg does not natively do that. For getting it to work you'll need to create a small apt repository (and ideally not on your device as reflashing will make you lose your setup).