There are many ways to create sprites. Many different software packages to use too. From Paint, to Flash, to Photoshop, to 3D packages.
If you have a tablet, then the best way for you would be to get used to Photoshop. You'll spend a lot of time cleaning up scans in Photoshop anyway. Plus, you'll have to create transparency so that could take a bit of time to get right by using a scan.
Either way, you'll end up doing a lot of work in Photoshop. For bigger sprites like Street Fighter Alpha and the like, sure it's worth the time, but for smaller sprites (16x16 - 128x128 for example), you're better off just learning to draw in Photoshop from the start.
You'll have automatic transparency if you create your sprites on their own layers.
Of course, you could just do the line art, scan it, and colour it in Photoshop and scale down. Search google for scanning and cleaning up line art.
Once you have your sprite, you can break up the body parts and use something like Spriter to create animations with the body parts. Although, it's best to create the body parts individually from the start (arms on their own layers, legs too, etc).
Hope that helps you get a better idea.