Upgrading your Apple devices - iPhone, iPad, iPod Touch - has always been a risky proposition. Though we found, with iOS 5, major problems may be avoided if you understand the process better and take a few precautions.
1. Make sure iTunes is upgraded to the latest version on your computer.
2. Clear off excess baggage from your device. As with any upgrade, you want to minimize what needs to be copied back and forth. The iOS 5 update actually backs everything up, wipes your device to factory defaults and then meticulously restores all apps, media and settings. Delete any apps you don't want any longer (this also wipes their settings including game saves, so be sure you're done with them!). Back up and clear off all of your camera photos and videos and uncheck any movies and TV shows you don't plan to watch anytime soon. Doing so might just save you from a drawn out upgrade like the 9 hours of updating and restoration required for our 64GB iPad!
3. Sync your device one more time manually to ensure you have all apps and media backed up.
4. Check in iTunes for how many apps, movies, TV shows, podcasts, music files, photos, ringtones and books you have installed to the device and record these numbers for reference. You can check at the end of the process to ensure everything was restored.
5. Disconnect and fully reboot both your computer and your device.
6. Put the device in airplane mode to reduce the chance of interruption.
7. Reconnect the device to your computer and start the iOS 5 upgrade in iTunes. If you planned ahead, you told iTunes to predownload the update (iPhone and iPad update are separate downloads, but you only need each of them to download once even if you have, say, two iPhones). If not, it will take maybe an extra hour to do this, depending on your Internet connection speed and how much traffic is hitting the Apple update servers.
Here's what to expect:
iTunes will backup your iPhone again - this appears to be a different from the backup you created yourself earlier with your final sync - and then it wipes your device completely and installs iOS 5. This is where things tend to go off the rails for people, since the process is a bit different from past upgrades and Apple still fails to provide an overview of the process or a meaningful progress bar that explains in detail where you are and what's going on.
You will notice that eventually iTunes pops up a generic dialog box that it is "restoring apps" but your device will no longer show that it's syncing. It may seem, especially after several hours of this restoration, that iTunes has hung. DO NOT DISCONNECT YOUR DEVICE. You can actually unlock it with the connection intact and go through the iOS 5 setup wizard, which prompts you to decide whether to activate location services and iCloud, pick your WiFi network and enter your Apple ID (more on this in a moment).
When you get to the Home screen, do NOT freak out. Chances are, many of your apps are missing and the ones that are there probably seem all jumbled and out of order. Let iTunes do its job. You can check the About screen on the device from time to time, but it doesn't seem to refresh as often as it should (particularly when syncing your media files later in the process). Don't panic. Just walk away and check back occasionally.
If you do disconnect (as we did with our iPad the first time through this process), you will get an error in iTunes. When you reconnect, it will skip to installing media and then, later, go back and sync any apps that it missed when you broke the connection. Those apps will be sync'd normally, so they won't be placed where you left them - but you should retain any custom settings/saved games. If you've filled up all of your visible screens with apps, this means you may need to go back and use iTunes to move them back the way you had them since iOS 5 still doesn't let you move hidden apps from the search screen into folders. We unknowingly broke restoration with just 20 games left to go on our iPad, and those were restored along game progress (yay!). But now we need to go back and try to put them back more or less where we had them.
Once you get up and running on iOS 5, it's up to you whether you want to use iCloud but keep in mind that only the first 5GB is free and then you have to pay for additional storage. You can always turn it on later in Settings on your device and configure what you want to go to cloud storage (we may try it with just settings). In the meantime, you can sync with your iTunes computer over WiFi - though you will need to plug your device into a power source before it allows you to initiate a sync.
A note about Apple IDs. If you use a different ID for Apple Store vs. Game Center and/or iCloud services for a secondary device, choose the Apple ID you want for iCloud/Game Center first (or create a new one for any device you want to have its own identity) and then change to the alternate ID in Store settings for iTunes Store, iTunes in the Cloud and iTunes Match if you share music and apps between devices.