should i put the air hoses on the powerheads so they take in air???
No, those bubbles are not good and will lead to problems with the fish's eyes (i believe).
i took it off only about 12" of glass in the middle is permanant
Try to get more gas exchange where there is no covering.
What kind of lighting do you have. If you want an upgrade for an FOWLR
, I would skip the skimmer, for now and get a lighting set up that sits above the tank. This will give you my gas exchange, and more stable pH....Maybe something like this:
But, that's just my thoughts.....