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.
In some cases, multiple degrees or diplomas at a bachelor’s level will award you one more point than a single bachelor’s degree.
Having said that, please use this tool to check the Canadian equivalency of your foreign degree http://www.wes.org/ca/evaluations/preliminary.asp?.
WES does not charge you by the number of degrees that are getting assessed, so I would suggest you send both Bachelors and Masters for assessment. If WES treats your Masters equivalent to Canadian Masters, then you get more points than just getting Bachelors assessed. On the other hand, if they consider your Masters equivalent to a Diploma and your Bachelors as Bachelors, then you can get more points by selecting the option 'two or more...' than just getting Bachelors assessed.