When you fill up questionnaire for FSW eligibility for your level of education would be "Two or more certificates diplomas or degrees one must be for a program of three or more years".
After that if you are eligible you will be able to create Express Entry profile. On that stage you have to create two separate fields for your two credentials.
For your bachelors degree, level of education would be your actual level of education "Bachelor's degree OR a 3 or more year program at a university college, trade or technical school or other institutes". Then you have this following question where you have to choose level of education according to your ECA report-
Level of education (Canadian equivalent) shown on Education Credential Assessment (ECA) report Your ECA report will tell you if your foreign education is equal to a completed Canadian degree, diploma or certificate. You must have the results of an ECA report to answer the question. Answer to this question again would be "Bachelor's degree OR a 3 or more year program at a university college, trade or technical school or other institutes"
In the second field you should enter your second credential. If it is a masters degree and ECA states as post graduate diploma then do the following-
Answer all the questions regarding field of study, duration, institute name, completed academic years and level of credential according to the actual details. after that fill all the questions regarding ECA and answer the following question according to the ECA report-
Level of education (Canadian equivalent) shown on Education Credential Assessment (ECA) report Your ECA report will tell you if your foreign education is equal to a completed Canadian degree, diploma or certificate. You must have the results of an ECA report to answer the question. Answer to this question would be "1-year program at a university, college, trade or technical school or other institutes"
Submit your profile you will be awarded points for "Two or more certificates diplomas or degrees one must be for a program of three or more years".
Hope it helps, Good Luck!