With all due respect to my esteemed colleagues, there isn't a BEST way to deal with windows in 144th or 200th scale, only a most PREFERRED way from individual Modelers. If you prefer your finished A380 to look like a solid airlines display or one of the resin/diecast models, which are ultra clean, by all means fill the window openings. If you prefer it to look like what you'd see sitting at the gate looking at it from the terminal window, make the windows transparent. Either/or, makes an attractive finished product.
If you do decide to make the windows transparent, there are ways of accoplishing this so the windows won't become concave over time, namely, applying a strip of clear decal paper that's been over-sprayed with Testor's Gloss Coat, once dry, apply coat of Future over strip... once dry, apply second clear strip and cover with Future, dry, THEN apply the kits' window decals and cover with Future. The clear material tightens as it dries like doped airplane fabric.
Another advantage of realistic windows is visible interior window shades and the occassional gawker's face, not to mention the "glass" appearance. The subject of filled/non-filled windows is a touchy point with airliner modelers, perpetuated mainly by decal manufacturers, but like I said it depends on the Modelers preference and either one looks great.
Take care and be sure to post some photos when you get going.
Frank