You can use different size tanks, BUT the water levels have to be the same in both tanks. If you have 2 tanks at different heights, then you can have different water levels relative to the tanks. <But the water level will be the same relative to each other ... or to an outside observer's point of reference.>
Depending on how you filter the tanks, ie if each tank has own filter, vs a flow through setup, there are further limitations on your water levels. <This is in case you lose siphon in the aqua bridge so you won't have a flood & fish on the floor.>
Have you look at the "fishy highway" site yet? They ahve some neat aqua bridge setups.
80 gal FW with 30 gal DIY wet/dry/sump.
9 fancy golds, 1 hillstream loaches, 1 rubber-lip pleco (C. thomasi), 3 SAEs, small school of white cloud minnows, planted.