As far as I know, they are not actually clear on this on the CIC website but it does have in the FAQ a question about it and they do say you can withdraw your old application and apply again under the new system. This is at
http://www.cic.gc.ca/english/information/faq/immigrate/skilled/skilled-faq09.aspIt does not actually say anywhere that I know of that you can't make a new application and not withdraw your old one but I think it goes without saying. They are trying to reduce the backlog, not make it bigger. If everybody decided to apply under the new system without withdrawing their old applications, that will do nothing to help the backlog, instead the same person may be taking even more resources. If you want to be sure whether you have to withdraw your old application or not before you apply under the new system, you should contact your visa office or embassy.