There's never a guarantee, but, using EBCI, I've never heard of families not being able to sit together. Of course, checking in at the 24 hr mark will usually get you all together, too, if you are a family of 3 and not picky about where you sit.
We used EBCI last year on a cruise vacation, even though it was just my DH and me, knowing we would not be able to check-in at the 24 hr mark and it was wonderful. We were about the 6-7th people to board and I didn't have to stress about getting us checked in or relying on someone back home to do it.
This year, we are using it both ways as we are a family of 6 going to WDW and my grandson is only 27 months old. He would not appreciate sitting by himself.

I also want to sit near him and his mom so that I can help out with him--keeping him occupied, staying with him if mom needs to go to the restroom, helping getting their gear on and off of the plane, etc.
Also, we have a very short layover (25 min) so I want us all to be together near the front of the plane so that we can get off ASAP to get to our connecting flight.
I noticed you said your 2 yr old will be sitting on your lap. If he truly is 2, he will have to have his own seat (and ticket). A lap baby must be
under 2 yrs old.