There is no simplified application process any more. Due to a large number of people failing to send their complete applications to the visa office within the deadline, I suspect often because of problems with getting a sufficient score on IELTS, immigration decided that you must send your full application to CIO. Those are the applications counted.
The CAPS came into effect on June 26 2010. They will be reset again on July 1st 2011. You can see the current status of the CAPS here: http://www.cic.gc.ca/english/immigrate/skilled/complete-applications.asp
Aside from the 1,000 per occupation, there is also an overall CAP of 20,000. Applications with a job offer are outside of the CAPS.