New to canister filters - help!

You should be able to contact eheim or at least get some technical support from their website at eheim.com.

That's exactly how I felt when I got into the hobby. My first filter was ECCO. Convinient but they don't explain much. Here's how I set up mine (I have ECCO 2234 that comes with three baskets). I put the blue pad in the bottom basket and filled the remaining space with effisubstrate. The middle basket was filled with effisubstrate all the way. The top basket-effisubstrate and the white pad on top. White pads need to be replaced once in 2-3 months. Eheim pads are relatively expensive so you can use regular floss instead. It works just fine. I do not change effisubstrate at all. I only replace the floss in the top basket and rinse the blue pad in the aquarium water. If you have a planted tank I would advise you to get a prefilter on the intake. That will help tremendously with the maintenance. The filter will not clog that fast.
Leaving the old filter in was a very good idea. As for the carbon, it's up to you. There are people that like using it and there are people that don't. I don't use it, don't see the point. In fact, a few of my filters have nothing but a sponge and floss. and the fish is doing great.

(IMO)use the floss in your pinguin & leave the subsrat in as long as it says is ok on box, dump out yucky chunks & with dirty water thats already in filter but leave them wet.substrat is smaller than biorings so u may have to jiggle them in fishtankwater, If they are realy messy they don't work as well,& I mean chunky mucky messy. if you use floss in your canister you have to change it alot ,& is easier to do so from your pingouin. also the charcoal is easier to plop in the pingoin if their is room(cover the charcoal with floss so its protected by it,that way you can change the cheaper floss a few times b4 changeing the charcoal) top with floss or the charcoal
.... so thats chemical & mechanical filtration in the pingouin & biological & mechanical in the canister, note the sponges in the canister will clog up quickly & should be in the 1st chamber then the substrat b4 your outflow (IME) you could maybe get eihime matrix for the last chamber. Matrix to me looked like a great new media. I always wanted an oldshool overflow filter for mechanical filtration good on ya

Floss is decent for short term mechanical filtration but should be thrown out often. Sponges last a long time and provide a great amount of surface area for bacteria to grow on. Just rinse them out every so often to prevent gunk from building up on them. And yes, keep the old filter running for now, that is easiest. But if your nitrites are high at the moment do a water change to get them low. Nitrites are big fish killers so the lower the better. And don't worry about hurting the cycle as the water contains very little bacteria, it is all growing on surfaces in the tank and any detectable amount of nitrite or ammonia means there is more than the bacteria can handle at the moment.

yah the floss you can toss easily & is the cheapest media ,the sponges need cleaning in aquarium water. bith are mechanical mostly & protect more expensive media from needing premature replacment like carbon