hi harryy
if you get PER you can always send additional documents to visa office such as(PPC,updated reference letter...)
if your initial reference letter didn't include responsabilities on it then i strongly recommend you to send the new one that you just got,this will help a lot for the visa officer assesing your application to determine your job duties and responsabilities.
dont forget to mention your file number,date of birth,name,uci number when sending additional documents to cic.
also depends on the the via office you choose in ur application you may want to wait for them to send you the AOR( acknowldgment of reciept),if your visa office is ottawa then just go ahead they don't really issue an AOR and you can opt for the file number issued by CIO from sydney nova scotia.
good luck