When I make trousers I find it easier to stitch the legs into tubes and only then stitch the legs together along the crotch seam. The only exception to this is if I'm doing high-spec fly openings with zips, facings and all that malarkey, which are always easier to do on the flat. Given that this is a pair of boxers and given you are learning, I would recommend the legs-first approach. It's a lot easier to see how the pieces go together that way.
Do note that when you come to position the legs prior to stitching the crotch seam you need one leg inside out and one leg right side out. The right side out one is slid inside the inside out one so you wind up with right sides together.
I make DH silk boxers for sleeping in and I've simplified them down so much they have no side seam and no fly, which makes them a breeze!