the way to tell what is in and out is to look at where the tubes go into the canister filter. there usually is a arrow going up and down. (down obviously in the inlet and up is the outlet)
I have never used a Fluval since i have a Ehiem (but they work the same). For filters and media there are several choices. The most common is some sort of carbon either through a carbon filter or carbon pieces in a mesh bag. I know Ehiem has a media that is hexagon shaped and one that it tube shaped. These are used like bio-balls for biological filtration. Ehiem also has a rock like media which works much like Live Rock in its a porus rock that is also a biological filtration.
What you do is if your working from the bottom up you would but a media (your choice), a foam or mesh filter, another media, foam filter etc. until you run out of space. I also used carbon as my last, but i dont know if thats required or not.
If Fluval doesnt have thier own media and filters you can buy any brand since they all work. Also, i would suggest not getting a "pre-cut" filter pad since they are about 10x the price of a large sheet of filter media and you can just cut it to size.
Any questions let me know since i've had my ehiem for about 6 years now. I now only use it for carbon and phosphate remover and as more flow, i did use it with all different media in my freshwater days.
Also, all you need to do to start it is usually prime it (get water in the canister and a syphion effect going from the tank) then plug it in. There is a pump built in the canister filter which will pump the water back into the tank.