Hard to say exactly will work for any system, but to give you an idea of what most people do for a light cycle...here's my schedule:
10:00am - Lunar LEDs on
12 noon - Actinics on
1:30 pm - Halides on
9:30 pm - Halides off
11:00 pm - Actinics off
2:00am - Lunar LEDs off
The goal was to gradually increase the amount of light hitting the corals by starting with the actinics, then going to full lighting before ramping down to just actinics again. I think most people follow that general pattern. Some decide to leave on lunar/moonlights 24/7...others allow for full a "dark period"...I can't comment on the pros and cons of either option, but since my tank is only several feet from where I sleep, I prefer to force myself to sleep with the tank going dark. If those lunar lights were on all night I'm sure I'd catch myself staring at the tank at 4am, lol
The duration of your photoperiod will depend on your tank...just watch for coral health and algae growth and adjust it longer or shorter as needed. I started with 6 hrs of full lighting, then gradually went up from there.
Depending on the design of your lid and your water level...you may or may not get salt creep. I prefer a lid because it keeps the fish in the tank and crap (pet hair, dust, etc) from falling in there. Yes, whether you go with a glass lid or a mesh screen you will block some of the light...but I doubt it will be enough to significantly effect the health of your tank, unless you are already on the edge of providing insufficient light for your corals. Absolutely true that a glass lid will increase tank temps. That being said, if you have a gap between your T5 fixture and a glass lid, you'll probably only see a small increase in tank temp. If that's a concern still, you can always use a mesh lid for the tank to allow for better ventilation.
Hope that helps
