You can add a line to the /etc/apt/sources.list file, which should do this for you.
For the following example, I'm assuming the following: you're using Lucid, your USB hard disk is mounted on /media/disk, and the APTonCD repository is in the folder "repo/ubuntu".
To edit the /etc/apt/sources.list file, type:
Add the following line:
gksu gedit /etc/apt/sources.list
Save the file and quit from gedit. Then, with your USB disk connected and mounted, type:
deb file:/media/disk/repo/ubuntu/ lucid main restricted universe multiverse
Your USB disk will now be added as a local repository.
sudo apt-get update