Did the old fan also have a light, or was it just the fan? Where are the wires from the light and the nightlight, are they in the same box? So you are saying that both conduits pictured run directly to the box on the wall where the switch is, i.e. there were 7 wires in two bundles running from the box to fan?
The three wires you see on the new fan are black (hot), green (ground), and white (common neutral). You'd normally just take the corresponding white, black, and ground/green (often a bare copper wire) and connect them to your fan. The lack of grounding wires is a little concerning, especially if the fan has a metal body in a humid environment. Where is the fan at relative to the tub/shower? If it's directly over a water source it needs to be GFCI protected. Are there grounds in the rest of the house?
I'd suggest opening up the electrical box on the wall and inspecting the switch for the fan. If it just has one red and one white wire attached to the switch for the fan, then I'd bet that the two wire conduit with one black and one red is your man. Also check to see if the rest of the wires have a third wire for grounding. Check your instruction manual for the fan to see if it has to be grounded.
As for that other bundle of wires...the best suggestion I have is to figure out what they do by some simple checking. With those wires disconnected, turn on the breaker and see if other lights, outlets, or appliances don't work in the rest of the house, if that's the case they may have junctioned other wires at the exhuast fan, in which case you'll have to pigtail them with the fan's in order to keep the circuit complete. I've never see 5 neutrals and only one hot...I really wish you could remember how it was wired.
Best of luck, let us know what you find.
EDIT: OH! Pictures!
So to clarify, it's 3 switches in one, right? So that means they used white for a hot??? Well if that's the case all bets are off I guess for correct wiring...
I'd say turn on the circuit, and using a tester, either no contact or a multimeter style, (be careful!) check to see which bundle of wires at the ceiling is hot with the bottom switch on or off.