I was checking out Finless' build videos, he goes over cutting the canopy for inserting the clear plastic shield, but whats the best method for securing the two together. Do I just use some CA on the edges? I noticed the instructions say to screw it together, but all of the pictures on the forums show seamless jobs.
So CA or is there a better alternative??

I always CA at four points on the windshield so as to not have globs of the stuff. Similarly to doing tack welds I guess.

I used Ambroid "Pro-Weld" on mine, and it worked perfectly! It is clear and thin like water, and it melts the plastic together, therefore you use it sparingly. Just apply a drop with the brush in the bottle's cap (or use a toothpick or similar if you need smaller drops) and hold the parts together for 10 seconds. It will not fog up clear plastic like CA will do, so I highly recommend it! Just be sure to use some masking tape or bits of electrical tape to position the parts before you apply the glue, because after about 20 seconds or so you'll have to cut them apart if they're misaligned. Oh, and the best part is, it won't glue your fingers to the part if you accidentally get a drop on you!