CIC did not have a straightfoward answer to this when I applied, and long story short, mistakes were made 
. My answer below is gleaned from going through a lot of forums etc as I did not know this while applying, and I certainly donāt know the exact way to do this on the cic website. Cic FAQ website is (was) unclear about this.
Hereās the gist: If you are counting your degrees towards the points then you need to provide ECA for those degrees. For e.g. if you are counting only your highest degree - PhD - towards your points, then you need to provide ECA for PhD only. But at some point during the application it will ask you for āadditional informationā and thatās where you have to disclose that you also have a BTech and a MS. This makes sense as you wont get any more points if you add PhD only vs PhD + MS as PhD will give you highest points.
Now I never tried it since I didnāt know at the time so I cannot tell you if it will work now or if theyāve changed anything. I would suggest, when you are creating your EE profile please make a trial profile where you can test this approach. As long as you are not hiding any of your degrees (a.k.a. misrepresentation) I think you should be fine.
When I applied I did not know this and I thought only my PhD and MS ECA will be sufficient but I had also added B.E. towards my points. They ācanceledā my application after a couple of months for this reason and I had to go through the entire process again but my B.E. ECA arrived just in time for the second application so I was saved. It did take two-three months for my Indian university to send the transcript the Univ of Toronto and I had to ask my parents to do the legwork 
Maybe someone on this forum has already used this approach and can answer this part of you question better.
Official transcripts are to be sent from conferring university (e.g., University of Pune, for me, not the actual college I attended) directly to the ECA agency.
For BCIT and Univ of Toronto (the ones I used), you need the transcripts (from your univ to the agency), degree copy and other documents. I did not have to send the actual marksheets to any agency. Your transcript should cover it. Call Univ of Toronto and ask them they have a good customer support.
Univ of Toronto does take time. When I applied WES was pretty much useless, maybe that has changed now. I did mine through BCIT which had the option of āRush processingā at the time, which I heard is no longer offered 
You should also try calling CIC helpline and see if you can get this answered.