For those who've been frustrated (as I have) by iAnnotate's quirky refusal to sync files that you download into it directly.
To get .pdf files from JStor, Project Muse, or another database into iAnnotate:
1. If you're on an iPad: Go into Project Muse, JStor, or whatever. Bring up the article in .pdf
2. Touch the upper right corner to get to the Open In buttons. DO NOT press Open in iAnnotate. If you do, you'll mark up the text for nothing, since iAnnotate won't save or sync it. Instead, press Open In and choose Dropbox.
3. Choose the destination in Dropbox and save it.
4. Once it's saved in Dropbox, select the file. it will open in the Dropbox window.
5. Click on the little arrow that's in the corner. Your options will be Print or Open in. Select Open In and choose iAnnotate.
6. Now that it's been loaded from Dropbox, you can mark up the article and the annotations will sync properly.
To get .doc and .docx files to convert and sync properly:
Short version: you can't do this any more.
It used to be that you could download a .doc or .docx file from Dropbox, convert it to a .pdf using iAnnotate, mark it up, and re-upload it to Dropbox using the tab at the top of the document.
Now, all you can do is mark it up and admire it on your iPad, because there's no way to upload the converted file.
There is a workaround: 1. do all of the above. 2. email the converted file to yourself. 3. save it in Dropbox. Why make us do the three extra steps, though?