How should I configure the wysiwyg filter to align the images?
Some people forget to turn off the built-in HTML Filter when they enable the WYSIWYG Filter.  If you double-filter, you will lose your img attributes.

For my part, though, I prefer to not put the float on the img; instead, I float the div that surrounds the image and caption, allowing them to float together.  (Example image, with floated caption "A battle...": http://www.westkingdom.org/content/new-members).  To give the content editors a good user experience, I allow them to set floats on images with ckeditor, but I move the markup to the div in a render hook when the content is displayed.  In this scenario, I don't need to allow floats on the image at all.

I have a writeup of how I achieved responsive images with captions using media 2.0, wysiwyg filter, and a couple other modules, and a couple of custom hooks.