is there a way I can control the colors while doing Skritter? Can I choose one individual color? I sort of throws me off everytime I see a new color show up

No; this is controlled by the tone colors option (plus being an alpha tester). It's on the list to make more tone color sets available as choices, but it won't be done soon, so if you don't like the current colors you'll have to turn it off, unfortunately.

is it the "color tones" option? I turned that one off but nothing seemed to change. The colors I'm talking about are the ones that I see as I'm drawing characters. The strokes that I draw are in a color other than black. What's weird is that sometimes it's just consistently black only for a while, and then all of a sudden colors start showing up as I'm drawing

It doesn't change immediately, but that is the option. The black ones are when it's going to ask you for the tone then, too, or if it's a neutral tone.