I've been running a red sea reefer 170 in a small apartment for over a year. I've learned a lot since then.
Anything I wish I did? Start smaller. At 40-ish gallons, a 5g water change doesn't quite cut it, and minimizing the amount of equipment required for a WC is key. Not to mention the difficulty in maintaining "enough" water on hand for an emergency.
I have an RO/DI unit sitting on the floor in between a toilet and the wall. I leave the lines ready to go - a faucet attachment stands at the ready on the counter top, and I roll up the waste and clean water lines for storage alongside the filter. When I need to make water, I simply screw in the attachment, unroll the waste line into the toilet, and unroll the clean water line into the bath tub where I fill two 5g jugs. I try to keep 10g on hand at all times. Not as much as I'd like, but that's all the closest space allows for.
Stack WC buckets then store the equipment inside the top one. I also keep two large Rubbermaid bins - I think they're 20g. I use them for emergencies (hospital tank, very large WC etc). I store equipment inside one, and the RO/DI jugs in the other. Collapsing everything like this helps conserve floor space while still allowing you to keep some larger containers and bulky water jugs on hand.
Not sure if this is the kind of information you were looking for or not, but I do hope it helps