An excellent rule of thumb for return sizing is filter length x filter width x 2 = capacity, so 20 x 25 x 2 = 1000 cfm and 18 x 18 x 2 = 648. You have a nominal capacity of 1648 cfm and a 5 ton unit needs 2000, so you are 20% undersized.
Your real problem is heat trandfer 101 - hot are rises, cold air falls.
Lets pretend that your 2800 sq ft house is the same up and down.
Each floor is 1400 sq ft, so you need the same ammount of air for each floor,
Hot air rises, so in the winter you need about 70% of the heat downstairs because the downstairs heat will take care of the upstairs.
Summer is just the opposite. The cold air downstairs pushes the heat upstairs, and the attic is hot as hell, so you need 65% of the cold air upstairs
you need some sort of damper system to make the switch between summer and winter needs.