The requirement states 'You should choose the highest level degree, diploma or certificate (or combination) that will award you the most points. For example, you would get more points for an ECA report that shows you have a Canadian equivalent of a master’s degree than for one that shows you have the equivalent of a bachelor’s degree.'
Based on the requirement, for the purpose of Express Entry, you need to get only your highest degree assessed by WES. Having said that, if WES requests your Bachelors credentials, then you may have to submit them, so be prepared for it. For the purpose of Express Entry, you can go ahead with Masters only.