Hi Nisha, I suggest you to send your documents to WES until then do not come to a conclusion whether your's would be considered as two or more certificates or masters. Even my M.Com showed up as one year graduate study where as after receiving my WES evaluation report it said one year post graduate study
. Now i can claim points for two or more certificates. My answer to your question here is, only in the CRS online assessment tool you will get an option to select Masters or Two or more certificates or bachelors just to know the CRS score. Whereas in the actual express entry system you do not have this option, it is like this, Education- Bachelors Degree B.SC ( In your Case) - Canadian Equivalency ( What ever you get from WES for your B.Sc degree ( can be bachelors degree three years/ four years) you should select that. And next you have to add your M.Sc - Canadian equivalency will be what ever the WES has accessed. If they unfortunately evaluate your M.Sc as one year graduate study you have no option to select one year graduate study therefore system will just calculate points as Bachelors degree due to which your CRS will drop drastically.
So i suggest you to send your reports, in my opinion if your specializations are different in B.Sc and M.Sc you may get your M.Sc as one year post graduate study and in your second education option you can select M.Sc and Canadian Equivalency would be one year post graduate study, now you are eligible for two or more certificates. Hope this helped you.
IMP: I have not yet got into the EE pool so based on a lot of research i am able to answer your question.