Hello and welcome.
When running a mixed light setup like the T5, MH combo depending on what T5 bulbs you have and what types of corals you are keeping the MH lamps will only need to be run about 4-6 hours a day. This will simulate the mid-day sun over the reef. After that the T5's and LED's provide the rest of light needed.
Glass tops have their ups and downs. They are great for reducing evaporation loss, and keeping your livestock that are prone to jump out in the tank, as well as keeping cats out. The down side is they tend to fog up and can significantly reduce the PAR levels at the bottom of the tank, or create hots pots if the condensation drops get too big and also provide a sweet spot for said cat to "sun" themselves under the MH's. They can also inhibit gas exchange as well since they are typically sized to cover the entire tank surface. If you do not have a cat, are not worried about evaporation, want as much of your usable light in the tank, but need to cover it, your best option is to use egg crate or make a set of screen tops with clear bird netting and window screen frames.