Oh sorry, it's for a 46 gallon glass bowfront. It will be freshwater. I've never used Matrix or Substrat Pro. Should I fill the middle tray with it? I've also never used Purigen. Likewise, should I fill the top tray with it? I'm thinking a coarse sponge and two fine sponges in the bottom tray.
Yes bottom tray one coarse than fine pads.
I would fill the middle tray with either one of those, just fill the tray no need to put it in anything else, and rinse it before putting into the filter. I am not sure how much the trays in your filter will hold.
The Purigen comes in a 100ml bag, that is all you need in a 46 gallon aquarium. Rinse the bag and put it in the top tray, it will not fill up the whole tray so you may add something around it like floss, or put a fine pad under it. When it turns dark you can recharge it in bleach and then rinse and soak it in prime before adding back in tank. It does not need to be recharged very often, up to six months. I would probably buy two bags, use on now, when you go to recharge it place the new one in, it takes a day or so to recharge and I do not like opening my canisters more then I have to.
Once you start using the matrix or substrate pro never rinse it in tap water, just fill a bucket with aquarium water and swish the basket in that if you want. Some people do the same with the filter pads, I do not, I wash mine in tap water.
By the way, I would have gotten the next size up filter for a 46 gallon, only because I have done this long enough not to listen to manufactures numbers.