Using my high school engineering... yes, you can place the fan into the existing duct, however I'm not sure of the air path, ie upside down Y or T duct work, or perhaps a side ways T.
Let me picture this in my mind, so if you flip one switch and both fans turn on, the air will blow upwards, if one fan is stronger than the other, it will dampen the flow from the weaker fan and possibly blow against the fan, as air pressure builds inside the duct. also I'm assuming one fan is located on a different floor, so the distance between the fans to the attic are different, which would also affect air flow.
This can be resolved by either placing a single larger exhaust fan at the attic, instead of 2 smaller individual intake fans. When you turn on the fan, it will suck air equally from each vent, depending not on distance, but the size of the vent. if one was 100 square inches and the other 50, then twice as much air will move though the 100.
I think the easiest thing for you to do, for just a few bucks, is to install a one way damper behind each fan, these dampers are used for laundry dryer vent to outside wall, are only $10 from home depot and made of plastic. the damper may not fit perfectly into your duct, but use your knife to trim it, then MacGuyver it into the duct with duct tape. Next, you'll have to use 2 independent switches, so when one fan is on, the other fan should be switched off. Only the moving fan will have an open damper, the off fan's damper would be closed. You alternate the air flows, I assume the aquarium fan will be on always, but if you do use the bathroom, the aquarium fan will turn off, thus closing it's damper.
I'm uncertain how you want to do it, but I hope I have given you some ideas.