Apps on multiple devices

Hi everyone. I am not sure if this is the correct forum for this or not, but here goes. Currently I have an iPad which I almost constantly use. I just bought an iPhone 4s each for me and my wife. All 3 devices will be under the same apple/iTunes account. I currently use apps like Goodreader, notes, as well as some others for work-related things. If my wife has these same apps on her iPhone would the data in them (mainly PDF files in Goodreader and notes in the Notes app) be copied onto her phone when we sync with iTunes? This would be pretty annoying since she doesnt need my work info and I likely would not be interested in the info in those apps on her phone. Thanks!