Link's bow should only be used for stopping projectiles. After Link's arrow hits the ground, it stays in the ground for a moment. While it is in the ground it will block all projectiles. Other than that, you should be using bombs the most with boomerang coming in second.
In Link dittos, just keep throwing **** and look for an opening. If you are relatively close to him, watch for him to go for a projectile, and rush him. Just rush in, and if he gets the projectile off, shield, and then continue forward. Link's projectiles aren't that helpful at close range (unless you already have a bomb pulled). They take a while. So if you are close and he goes to pull one, bum rush him. If you are far away, slowly approach with projectiles, shielding those from him. You'll eventually get close enough to hit him.