Hi. "Speaker-level" connections refers to the connections that use speaker wire, like the ones that you use on the Marantz to connect to your Q300 speakers. The RCA connections are sometimes called "line level" connections.
You want something in your system to direct lower frequencies to the subwoofer and the higher frequencies to your bookshelf speakers. Because your setup currently doesn't have anything that will do that, you can have the sub do it. In order for the sub to do that with your other equipment, you'll use the speaker connections. Basically, you'll connect the speaker wires from your Marantz to the sub, then connect speaker wires from the sub to your bookshelf speakers. The sub will filter the low frequencies out for itself and pass on the other frequencies to your bookshelves.
The sub would have speaker wire inputs, speaker wire outputs, a crossover dial (that you'll use to set which frequencies go to the sub and which go to your bookshelves), and a volume (or "gain") dial. An example is shown below.