I am trying to change the color in my comments box to anything but bright white, because I have a dark background. I figured out how to change the color of the box around my comments box, but not the comments box itself.

An example page is: http://www.nathannagelkerk.com/welcome-5

There are 3 rectangular boxes and 1 big white box. I'd like it to be a shade of grey.

Just to clarify, I'm trying to change the color of the rectangular boxes as well.

I fixed the comment box color by adding this code to my stylesheet.css:

ol.commentlist li {background-color:#000;}
form#commentform input, form#commentform textarea {background-color:#6A6A6A; border-color: #6A6A6A}

Now the problem is that there is not enough room for the avatars, and this is the Theme's fault. How would I fix that?

I turn the avatars off. My theme must not have been up to date with the wordpress updates, because the user name under the avatar was running into the next avatar. If anyone knows how to fix this, please let me know.

You are not using the AQtahualpa theme - why are you asking this question here?
if you decide to use Atahualpa and have questions using this theme, feel free to ask here. If you problems with another theme, you go ask it's author