How do I change the highlight color for selected text with Emacs / deftheme?

What you're looking for is the region face. For example:

(set-face-attribute 'region nil :background "#666")

In addition to tungd's solution. You could also then change the font color to make it more readable. E.g. to white

(set-face-attribute 'region nil :background "#666" :foreground "#ffffff")

You can use the customize interface.

M-x customize-face

When prompted for which face, enter region. Then you'll see something like:

Using customize makes it easy to experiment with lots of colors. Try clicking [ Choose ] to access the color-picker), then [ Apply and Save ]. It also nicely organizes your customizations into a single file (rather than further polluting your init.el).