There may be a way to get points with your PNP nomination. Not really sure as the information provided on CIC website is not very clear. Best way to find out would be to start the online profile for EE and see if they ask you about the PNP nomination and if that does anything to your points. If it does then you should get an extra 600 points for your PNP nomination. Hopefully that would be enough to put you in the higher end of profiles and get you the ITA.
My understanding however is that PNP certificate holders still apply the way they did before and that is with a paper application that they mail into CIC. Nobody is really sure how the new EE system will affect that PNP applications that are received by mail. The hope is that the EE system will speed up all CIC application times. PNP applications use to get priority over many other streams (that is why you get that sticker) but nobody is really sure how that will apply now with the EE system. Will PNP applications be given the same priority as people who get ITA under the EE system? Or will they have basically have lost the priority they once had to the EE applications? I am hoping that either way the entire CIC system is now more efficient and therefore PNP applications are faster.
Keep in mind that even if it give you the points for your PNP on the EE profile and that it promises to have you PR within 6 months of actually applying that the 6 months if from the time you apply for PR not the time you set up your EE profile. You can't apply until you get your ITA and you may have to wait months to get the ITA. In reality nobody really knows what other people's profiles look like so you can't see your competition to know what your chances are of getting ITA each round. I also don't think anyone knows how many profiles they are giving ITA to each round. And even if someone sets up a profile after you it they have more points than you they will get the ITA before you. So basically you could just keep on getting bumped by stronger applicants and never get the ITA.
If you apply on paper just with your PNP and not through EE then there is no time line available as to how long it could take to get your PR. Because of the changes any applications received after Jan 2015 don't have an estimated time line because they don't know yet how the new EE will affect the CIC system as a whole.
My boyfriend and I thought long and hard about trying to apply via the EE with his PNP nomination but decided on proceeding with the paper PNP application because doing the EE would mean one more step and there was no way to know if in the long run it would make things faster. We only knew it would mean one more step. Also the PNP certificate has an expiration date and if you don't get your ITA before that you could risk loosing your PNP. Remember there is no time line on when you could expect an ITA after creating an EE profile.