Updates and affects to what ? iOS updates tend to include fixes and security updates, and for larger updates (e.g. iOS 4 to 5 or 5 to 6) new functionality (though iOS 6 also removes the YouTube app).
iOS 5.1.1 update details : http://support.apple.com/kb/DL1521
iOS 6.0.1 : http://support.apple.com/kb/DL1606
iOS 6 is not available for the first gen iPad
If you mean something else ... ?
It hasn't messed mine up. Whenever I update mine I always make sure that I've backed up everything first, so that if anything does go wrong with the update process then I've got a copy of anything that's important.
What model iPad do you have ? If you have a first gen iPad then the highest iOS version that you can update to is 5.1.1 (it doesn't support iOS 6). An iPad 2, 3 or 4 will update to iOS 6.0.1 (iOS 6 removes the built-in YouTube app and the Maps app changes).
To update via your computer, connect the iPad to your computer's iTunes and copy any purchases off the iPad to your computer via File > Transfer Purchases. You may also want to copy photos and any important documents off the iPad as well e.g. via the file sharing section at the bottom of the device's apps tab when connected to iTunes, via wifi, email, dropbox etc - they should be included in the backup, but it's best to have a copy of them outside of the backup just in case. You can then force a backup of the iPad by right-clicking the iPad 'Device' on the left-hand side of iTunes and selecting 'Backup'.
Then start the update by selecting the iPad on the left-hand side of iTunes, and on the Summary tab on the right-hand side clicking the Check For Updates button
Updating to iOS 5+ : http://support.apple.com/kb/HT4972