The process following submission is provided at the CIC website - an extract is provided below. While it does not explicitly state as to when the CC/BD is charged/encashed, you can from the choice of words used deduce that it happens after “Completeness Check” but before the end of “Eligibility Review”. While the former states at its concluding sentence that “your entire package (including your payment) will be returned to you”, the latter states “...confirms that a refund for the processing fee will be issued”. The use of “returned” and “refund” makes this distinction.
EXTRACT FROM CIC WEBSITE
http://www.cic.gc.ca/english/information/applications/guides/EG77.asp
Completeness Check
Citizenship and Immigration Canada reviews your application to make sure that:
• all required fields in your application forms are complete,
• all required documents are submitted from both the CIO document checklist (IMM 5612), and visa-office-specific document checklist
• the correct processing fee payment has been made
If your application is:
• incomplete or;
• the occupation you are applying under has reached the allowable limit under category 1,
your entire package (including your payment) will be returned to you with a letter explaining why it is being returned.
Eligibility Review
An officer will make an final determination of eligibility of your application to determine whether:
• your application qualifies for processing under one of the two categories described in the Ministerial Instructions
If your application qualifies for processing, you will be sent a letter that :
• notifies you of this fact and provides you with your reference number.
If your application does not qualify for processing under the Ministerial Instructions you will be sent a letter that:
• provides the reason why your application is not eligible for processing
• confirms that a refund for the processing fee will be issued
Selection and Admissibility
If your application is eligible for processing, your application will be assessed against the following requirements:
• minimal requirements
• selection factors
• required funds
• admissibility (criminality, security, medical)