Returns in the basement will make a world of difference. Especially if they are place near floor level. I would insist on that. Are the Lennox 2 stage variable speed units?
It would help comfort levels if they were. Being able to run the fan on constant at a slower speed will help the comfort level in the home.
I would recommend you doing your own heat loss. With out all the specs on your home it is hard for us to know which contractor is correct on the sizing.