1) I want my "categories" list to be listed on the left side, underneath the header
All of your posts are currently using the "Image" post format, and categories aren't displayed for those posts. Please switch at least one of the posts to the standard format in order to see the categories.
One way to move content around in a layout is to use absolute positioning. It's not a perfect solution because it requires that you know the exact position where you want the content placed and will be the same for every single case. For example, if you setup the categories to display just below post titles, that assumes you know exactly how tall every post title will be. If you had any really long post titles that fell over onto two lines, it would overlap with the categories. Here is a basic absolute positioning block which I tested on a plain Toolbox setup with no other custom styles. You can test this out and adjust it to see how it works:
.post {
position: relative;
}
.post .entry-meta .cat-links {
position: absolute;
top: 2em;
left: 0;
}
Note that your CSS will probably need to be adjusted to take any CSS you have added that affects spacing and layout. Experiment with the top value until it fits in your setup.