I'm confused about the question- are you asking about submitting the FBI PCC to CIC after the eAPR has already been submitted? Or are you asking just about a general situation where you need the FBI PCC, but you can't get it on time because the ITA deadline is 60 days, and the FBI PCC can take 12-15 weeks to be processed?
In both situations, the best bet is to request an FBI PCC as soon as you get the ITA, and then complete your CIC application and submit it with a letter of explanation in lieu of the FBI PCC explaining how you tried your best to get the PCC on time, but can't, owing to FBI's processing times. Attach any proof, such as receipt of your sending the request, as well as any tracking information, to the letter, too. This should get you a 60 day extension. If that is still not enough, you can request a second, longer extension from CIC when the time comes, too.