We live in a 3 level, small single family house. We are replacing our heat pump and air handler -
We want to know if a 2.5 ton unit (either in or out) can be paired with a 2 ton unit. Do they both have to be the same amount of tons?

Depending on the manufacture, you can usually make it work. You may have to adjust the blower speed to increase or decrease the cfm. To be safe you should check the specifications to see if they will match up. With a 3 level house I would guess that you need at least a 2.5 ton unit.