PR doesn't depend on what course u took however ur PGWP may depend on where u took the second course and if ur college is eligible for PGWP. PR depends on ur level of education, ur english score, ur job(skilled job level NOC code), ur past experience etc.
Level of education means Masters gets more point than PG diploma, PG diploma gets more points than just bachelors and so on. for better understanding use the calculator tool provided by CIC
http://www.cic.gc.ca/english/immigrate/skilled/crs-tool.asp
