I've done it both ways, and here are the pro's and con's.
If the armor is glued together first, you don't have to worry about the 2 helves matching up (because they are glued). But you have to be really really careful when cutting through 2 layers of plastic because even though I am very experienced with a dremel it was a bit unnerving.
Obviously if you cut the 2 pieces separately, cutting goes easier, and I think it is easier to sand because there is less bulk to manipulate. If you do it this way triple check your measurements so your 2 pieces line up after your cut them.