It was done and hopefully going to be like this:
1 - They first open the package, check if all required signs are done, all required documents are present, and all fields are filled. IF YES, than goes to next stage, IF NOT, they pack again, and send back.
2 - This stage, a Visa Officer at CIO decides the completeness of the application including matching job duties, calculating points and stuff [basically he goes through all of the documents what we have sent]. If you pass this stage, than your CC / DD will get cashed, a UCI will be assigned, and you will get an AOR, and your file will be transferred to respective visa office [will take few weeks for all these]. Beyond this stage, if get rejected, no refund will be made. IF CIO VO officer decides that something is missing, or job duties are not matched, he'll prepare a rejection letter, and you will get your application back without getting charged along with letter.
3 - Local CHC VO than studies your case, and basically all the Background checks, medical, Passport and stuff are done in this stage. If everything is okay, RPRF is sent and Issues a Visa. If something gets wrong, gets rejection and no fee refund.
That's it.