Ok on the honey flow under the roof thats sits on the super there is a cap / plug on it. I understand it helps with ventilation but if left off will the bees start making honey combs in that are under the roof. Sorry for the weird questions but this is my first time doing this and want to get as much knowledge as i can before i introduce my bees to the super.
Hi Gary, my advice may differ from others. My suggestion is to leave it open, however it involves lifting the roof once a fortnight to monitor the roof area.
My main reason for leaving the plug out is to give the bees a relief valve for when the population explodes. By lifting the roof once a fortnight, you’ll see when that starts to occur.
Hi Gary, around here we call that an inner cover. I think Jeff’s use of it as a predictor of a colony’s readiness for more space by leaving the plug out is a good one, provided you do check frequently enough to keep up with nectar flow. It’s also fine to tack or rest a piece of screen over the hole so there’s airflow, but the bees can’t come up and build comb in the roof space.
I leave the inner cover holes open on my hives except in winter when I add a shim and insulation on top/under the roof (outer cover). During the spring and summer I find that the bees will use the top surface of the inner cover to make ‘beetle jails’ - propolis-honey structures that look like little igloos where they corral small hive beetles away from the rest of the colony. I’ve learned to be ready with my hive tool or gloves finger to smash as many beetles as I can when I lift the roof - their bee jailers get distracted and the beetles have a chance to make a break for it 
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Last summer I put a piece of mesh over the inner cover that was too small for the bees but big enough for the beetles and the a piece of (fuzzy side up) vinyl above the inner cover and caught quite a few beetles. That way I could also lift the roof and smash beetles without disturbing the colony.
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Nice one, Alok - your bees are probably chasing them up there, and the trap means they don’t have to keep watch 
Edit: noticed in my earlier reply I wrote propolis-honey structures, when I meant propolis-WAX.
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