When you send your application it passes by several phases..
1st phase: Completeness phase:
The CIO officer checks that your application is complete & that all the required documents have been supplied.
They then encash your Credit card or Bank cheque.
(so if your payment got encashed, that would mean that you passed the first phase, where you application was found complete.. & that's usually done in a week's time, sometimes it took 3 weeks, though not common.
If your application was found complete & your cheque got en-cashed they start eligibility review in CIO.
If unfortunately the application was found incomplete they do not encash the cheque & they resend the application back by regular mail which takes from 1-3 months to reach the applicant
2nd phase: CIO eligibility review phase:
The CIO officer checks your papers & ensures that your NOC follows the ministral rules. He also counts your points.. & makes sure that ALL papers follow the eligibility criteria, with the IELTS and all..
If the officer finds your application eligible & everything is fine, he gives you a
positive eligibility review (PER) & transfers your application to your relevant Visa Office, then sends an email if the applicant supplied an email in his application (in which there is your file number & client number) to inform you of that.
If unfortunately the application was found not eligible (NER) for processing (e.g. not enough work experience, not enough points) they send an email by that informing the applicant.
That usually occurs 30-120 days from the day you submitted your application.
In this phase, & after you recieve a file number/client number, you can start checking your ecase status (online application status) from the following link
https://services3.cic.gc.ca/ecas/?app=ecas&lang=en
3rd phase: The VO: (differs a bit from one visa office to the other, but the following is in short)
2nd AORs sent (by email or mail according to VO),
Another fast eligibility review is being done, background & security checks. Medical Request, Police certificate request, Request for Permanent Residence fee & Passport requests (by mail).
If unfortunately anything is missing, they will contact you (probably by email, sometimes by phone calls)
Ends by issuing the visa 
soon inshAllah (by god's will)
You can follow the post 26 June applicants time-lines through this spreadsheet
https://spreadsheets.google.com/ccc?key=0AiJy8Qu8lcQbdGxiSnNhME5sVi1uRlZtUWNhOEFwemc&hl=ar&authkey=CLDXsFA#gid=
This website is from one of our forum members (Wayne), a good one, you can have more information from it as well..
http://get2canada.wordpress.com/
another sweet blog from another forum colleague (Indira):
http://indiraprabhakaran.com/blog/
best wishes,
basmalahh
.. If you have a file number, you can check the online status of the application from the below link.
