I believe the instruction manual calls for the side windows to be glued on the inside of the fuselage (I no longer have the manual). But I am certain the windshield seam will look stupid showing on the outside but the side windows not showing any seams. How do you blend in the windshield, which obviously has to be glued on the outside of fuselage, with the side windows glued on the inside. Or in other words, how do you hide the seams (and the canopy glue) on the windshield?

Don't sweat it. You'll never see it at 500 feet

Use a real thin bead of E-6000 glue. It is transparent and will hold your windshield on with a bead only as wide as the windshield is thick. Additionally you can paint E-6000 to match the color of your plane if you so desire.