Things I have found out so far, I'd be grateful if those who have used it in anger can add their experiences:
The appraisal goes to the 1st RO first, not the subject. The two boxes on the old F6000 that the subject used to fill in before giving it to the 1st RO are automatically taken from your JPA preferences (You did all know you had to fill in your career aspirations on JPA didn't you?!) - in case you missed this you can add them in after the report has been raised by entering the data on JPA then asking the 1st RO to click the manual refresh button.
Copy and paste from Word into JPA will save you countless hours of pain. In my experience JPA is unbearably slow and prone to dumping you out of the report writer without saving your data. One gotcha here is if you try and paste too much text into the box nothing will appear at all, even if it is just one character over the text box size.
The promotion recommendations page is very confusing, do I have to fill in all the boxes? Eg the ones on specialist employment?