The main concern I see with running plumbing under the floor is water than has to flow uphill, and that's always a struggle. Can be done, but you'd need the fuge to be pretty high.
I put my tank in my office specifically so I could run piping through the wall into the garage. The downside is my office isn't very large, especially with the tank in it lol! It's worked out well though.
Good luck with your remodel. I finished off the basement of our last house myself doing everything but the carpet. It's a ton of work.
Regarding equipment, I've been pretty happy with everything I've chosen. The return has been rock solid, as has the skimmer and power heads. I cleaned the gyre for the first time earlier this week and flow did noticeably improve, so I need to do that more frequently. I just haven't had enough coral to test the lighting long term, but it seemed fine before the dino's and vermetid's hit. I'll supplement with T-5's if/when the time comes where I feel I need more kick.
If only I could redesign the entire house and build a fish room!
I will be following yours! Thank you for all the info. I'm sure I will be asking lots more!