What I have heard from majority of people, is that if MBA in India is from IIMs, only then WES evaluates it as Masters degree. MBAs from all other universities is evaluated as Post graduate diploma.
Coming on to IQAS, many people have stated that IQAS evaluates all Indian MBAs as masters. Going by that, you will most probably get Masters from IQAS but still we shouldnt rule out the worst case scenario.
Moreover, if you plan to use evaluation by two different agencies in combo, it will cast some doubts and can even cause problems in future.
So, best is to get both degrees evaluated by IQAS.
If, you want only MBA to be evaluated by IQAS, then do not mention you Bachelors WES evaluation in express entry profile at all. That will be a sureshot invitation to rejection.