The only way to store apps on a computer is iTunes.
You can point iTunes' Media folder to a different drive on the computer by going into it's Preference, the Advanced tab.
You should be able to simply copy the current iTunes library to the new drive, then repoint. But make sure it's a copy, just in case something goes wrong. You can then point it back to the old directory.
If for some reason the new library want's to erase the iPad, cancel that dialog, right click on the iPad under the devices list, and choose Transfer Purchases. You'll have to do this anyway to make sure all you current apps are copied to iTunes.
While copying your apps (and other media) to iTunes is a goods secondary backup, in most cases it is not needed.
All your apps, iBooks, iTunes Music, and most other media purchased through Apple can be re-downloaded directly to the iPad. Just go to the Purchased tab in the appropriate store. Or your can search for the app. Apps and content that you have already purchased will say INSTALL (or maybe Download) instead of showing the price. In some cases they will have a cloud badge on the icon to show they are not currently on the device, but available for download (at no cost).