Well the period to submit applications just ended for the majority of schools…
Here are some colleges with later deadlines:
http://time.com/money/3652370/best-colleges-late-application-deadline/
The Common App does not submit all your applications all at once. You can submit only one application at a time. For more information on the CommonApp, I suggest you acquaintance yourself with CommonApp’s Applicant Help Center: https://appsupport.commonapp.org/ics/support/default.asp?deptID=33013&_referrer=https://www.google.com/url?sa=t&rct=j&usg=AFQjCNFAkE0dGIzzQQGWyCVR8Y1jKN59mg&q=&esrc=s&ved=0CCAQFjAA&url=https://appsupport.commonapp.org/&source=web&cd=1&ei=jOm6VNGuCvGxsAStwoCADw&sig2=2jBqMXetvJZK8CX_J1n05Q&bvm=bv.83829542,d.cWc
To answer your last question, CommonApp is used by over 517 colleges while only CUNY schools use the CUNY application. There is not so much a pro and a con to each as most schools don’t give you the option of which to submit. Some schools do (Columbia) though I don’t know why you’d want to fill out all of that information again if you’d have to fill out the CommonApp anyway for other schools.