All the themes seem to have the Logo placed left justification. Is there a way that I can right justify my Logo?

You could use an png or gif image as wide as your shop and have the logo on the right hand side with the rest transparent. You could also use it in the header background instead. There you can adjust it's position better.

Thanks for the tip, I'll try that.
One would think that a logo could be placed anywhere.

OK, that seems like it will work out ok.

Some themes have the navigation bar below the logo, other have it inside the same box as the logo, I don't see how this is accomplished. Are these things embedded into the theme? I can't seem to locate the images used either.

Yes the images end up being part of the theme when you alter it.