You need to go into Preferences and devices, you put it to where when you hook up a device like an iPhone or iPad and it won't sync with your iTunes so you check "Prevent iPods, iPhones and iPads from syncing automatically." So when you hook it up it will just show the device and you can do whatever you want like back it up to your computer or even transfer purchases. All it does is add the apps to your iTunes and any other thing you decide to sync over to iTunes like music or videos.
I have my iPod Classic and my iPhone 4 connected and they never sync or do any deleting. You can add your iTouch apps to your iTunes with transfer purchases. With an iPad you can just download the apps from the store and just transfer purchases when you hook it up. I stopped using the Wifi connect because iTunes has been having issues with it opening a program called ATH.e.
iTouch apps can work on iPads but there are usually updated apps specifically made for iPad usually they will be called like HD at the end of the app. With iPad I just download the apps through the device itself and just arrange them on the device and never mess with iTunes. I only use iTunes to back up, add music and stuff like that. I do all my app updating and downloading from my iDevice.