I say cover.. with individual panels. Esp with Lexan windows - yes, caution is required to avoid scratching, but without they will be opaque in 7-8 years. We have a 6 yr old dodger with lexan, we keep the covers on in port and the lexan is still like new (aside from the inevitable scratches, in this case not from the covers) Individual covers allow you to provide some shade now and then but not cut off all the light, or the visibility.
On our last boat we had an overall cover.. after a while we quit using it because it shrank and wouldn't fit and the windows went opaque and looked awful in a relatively short time.
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)