For some reason the motion blue on photoshop is messing up.

Also is there a transparaent tool in photoshop like in paint?

(The transparant tool is 7 down from the text tool in the picture above)

it doesn't convert because ps uses transparent layers. paint doesn't

What should i do?

work in photoshop

Lets say my background is black and i have a sprite on a black background. When i use the select box to select a sprite. When i drag the box over the sprite the background is going to be selected with it. How do i get rid of it.

You're only working on one layer. If you made the blue balls on a separate layer from the black bg, then it wouldnt select the black bg as well. The best advice i can give would be to select as closely as you can. Try to get JUST the ball in the selection, nothing outside of it.

you can aslways use the circle lasso to select the ball and move it

When you put the comic in photoshop, copy everything below the comic and put it on a new layer, and then delete the black space with the tool. Make sure tolerance is 0, opacity is 100, and all the boxes are unchecked.

You can also use the magic wand tool to select the background around the balls, then go to the Select dropdown and click Inverse. That will Invert the selection so only the ball is selected.

(At least, I'm fairly sure photoshop has the inverse tool)

It does, and for reference it looks like this.