i would use spaflex or another flexible tubing for return from sump. it will cut down on head loss and if you ever have to move something, it moves quite easily- no unscrewing or sawing pipes apart.
clear tubing will grow a lot of algae in it. it won't be clear for very long.
a length of pool hose is fine for drain.
i like the refugium after the skimmer but before the return section. any pods
will have an easier time making their way to the dt, not having to go through the skimmer section.
i put the bubble trap after the refugium and before the return section.
the overflow and return pumps need to be strong enough to power whatever mechanical filtration you have in the sump. in other words, if you have a skimmer with a 400 gph
pump on it, you will need at least 400 gph
for it to work efficiently. i would not use the return pump for flow in the dt. more than likely, you'll just be battling a micro bubble issue.
finally, i would have more than 1 power head in the dt. if you are concerned with aesthetics, buck up for a single vortech mp 40.