By looking at the updates available in the App Store on your device, you will see what works on that device. Then you got to iTunes and update only those, ignoring the rest. If your iDevice has iOS 6, there aren't many that you will have to ignore - for now. My iPod touch 1G now has dozens of updates that don't work on it, since it is topped out at iOS 3. So I ignore all the updates listed until one shows up on the App Store on the touch. Eventually, my iPhone 3gs will reach that stage, too, and by checking the App Store on it I won't have to check each update listed on iTunes to see if it will still work on iOS 6.
If you have devices with various iOS versions, it would seem to make sense to have separate accounts for each. Why not? It may be clumsy, but it saves hassle figuring out which app works with which device. And I have a separate loging on the computer for each device, too. Which is easy for me, really, since I have just about given up on updating anything on the touch! And it give the the opportunity to have different music libraries, too.