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<div class="column-one">
<div class="section">
<h1>Category One</h1>
<ul>
<li>Entry, Title</li>
</ul>
</div>

<div class="section">
<h1>Category Two</h1>
<ul>
<li>Entry, Title</li>
</ul>
</div>
</div>

Entries will be placed between <li></li>, each section is a category with it’s entries. I want to be able to change the ordering of sections. For example category one should be above the second category and in the opposite order. Any ideas how to make this? Thanks.

I don’t know why, but this throws me for a loop:

For example category one should be above the second category and in the opposite order.

You want category 1 to precede category 2 in the markup. What is in the opposite order?

Also, do you have some template code you’ve tried to far? That can help see what you’re getting at. Psuedocode can too, where you try to talk through what you’re trying to accomplish.

EDIT: Also, maybe category_archive is what you’re looking for?

http://expressionengine.com/docs/modules/weblog/category_archive.html