1) In the reference letter, can my boss copy the exact SAME duties from the cic website or does he have to change some wordings ??
Your boss should write the truth, what are the responsibilities of the position, in his/her own words. In fact, you SHOULD have a written job description anyway, that your boss can cut and paste.
BUT if he copies directly from the HRSDC (not CIC) website for the NOC, it will be a "red flag" for CIC and could be rejected.
2) can i submit the reference letter and pay stubs to prove my employment ???
You MUST submit the Letter of Employment, per the instructions for application. Pay stubs are not required. Refer to the application instructions and Document Checklist.
http://www.cic.gc.ca/english/information/applications/cec.asp
3) When i started in the fast-food, i was a shift manager right away, so do i still need to put the position held during the employment and the time spent in "EACH" position. Because, i only held "ONE" position which is shift manager and not "OTHER" positions like supervisor.
I'm not sure what you're asking. If you only held one position, then you only held one position. It's not uncommon.
4) What kind of format should the reference letter be ????
There is no fixed format, it is simply a letter that can follow any standard business format. The Letter of Employment must simply contain all the required information as described in the document checklist.