I'd like to learn

[Level 1]

Well, I think people would like it if you were to start your sprite topic off with some work you did already, but I'll help you out of this one.

To start off your question, any image editor would do the trick. More advance pixel art techniques that involve transparent pixels and layers need Photoshop (or GIMP). Otherwise, regular old MS Paint would do the job (even Gors and Vipershark use it).

As for placing the pixels manually, you have to do that. I know it sounds like a chore, but that's part of the charm of pixel art creations. All you need to do is rough out some flat shapes, use darker and lighter colors to provide the shading and highlights, and then you're done.

I was just about to edit my post and comment on some of the points you made here. It would help for us to see your level of work, that way we can point you to the right direction.