Small dog, close up - you're going to have a shallow depth of field no matter what. Try to get the eyes sharp and the rest is less important.
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The 50 f/1.8 will be sharper than the kit 18-55, but if you use it wide open to get a faster shutter speed you'll just get an even shallower DoF. Used at the same aperture as you'd use the kit zoom, it'll give you a better straight capture. So boost the ISO, especially if your dog's a wiggler.
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(resized only; Neutral Style ISO 1600, 1/80" at f/3.2; 24-70 f/2.8 on 1D 3)
Don't be afraid to use the flash as an accent; it'll add catch-lights to his eyes, which help perk the shot up. Be careful about letting it overpower the ambient light, though. Sometimes the black background can work, but it's hard to predict how it'll look. In your example, the strong directional light and black background works pretty well, but a little bit of fill light on his left might have helped round out the shot by filling in the left side of his face. It doesn't need to be strong, just enough to bring it out of the overall black background. Tanner, Tyler and Buddy were all shot with bounce flash and a kicker to get some of the light directly into their eyes. Luca was entirely available light.
AWB does OK in most lighting conditions, but it's documented in your manual that it only works down to 3000K, and most household lighting is at around 2800K, so your pictures will all have a warmer cast than they should.