iTunes is the tool to update, backup and sync your iDevices. You will want to do this once a week to get updates and backup the settings on the iPod/iPad.
If you are syncing the iPad or iPod to your reimaged computer or for the first time, you will need to Authorize the iTunes program ahead of time and Transfer Purchases to the computer.
Apple Article: http://support.apple.com/kb/HT1848
Periodically, Apple will release software updates for the iPod or iPad. You can check in iTunes by connecting your device and then clicking on the Check for Updates button.
When there is an update, iTunes will download and install the software update.
iOS 5 is a MAJOR update and can take hours, please check here for more information.
iOS 6 can be done with iTunes or over wireless. It is recommended that you plug in the iPod/iPad to power before running an iOS update.
The software update process can only be done on ONE device at a time and can take a very long time. ~45 minutes
Great Page from Canby, OR K12 site on dual-account syncing:
Syncing Multiple Accounts in iTunes link to other site