Goodreader has "Open In" capabilities, so you can open your document in iAnnotate from your Goodreader app on the iPad.
On the iPad, when Goodreader/your document is open, tap on it to get the menus open. In the bottom right, you'll see an arrow. Tap on that and you'll see an "Open In" option. Once you tap on that, you'll get two options: (1) to open the file "as is" or (2) to "flatten" the file (hard bake any Goodreader annotations you've made).
Pick which one of the two you want to do and you'll get a menu of apps that you can open the document in. iAnnotate should be one of those options and once you select it, it'll open right up.
Then, you can switch back and forth between them. You can also save the file in iAnnotate after you've opened it from Goodreader (no iTunes necessary).
Hope this helps.
Marilyn
