The key to pane structure is to create the layout in HTML and CSS first, this will give you a clean set of divs and the CSS to achieve what you're looking for. Based on the example you've supplied this looks like 6 divs with a clearing div between the 3rd and 4th. For div 1 and 2, 4 and 5 float these to the left and give them a width and add whatever margin you need to divs 2 and 4, then float 3 and 6 to the right and give them a width as well.
Regarding the use of containers, these are wrapping elements for the modules you insert into the DNN panes, and are used to add style to the module. The amount of style can be as much or as little as you like, and the containers have skin objects as well such as RSS icons, Max and Min links, menus and the Title.
You can include as many containers as you like in a DNN page, and the container can be set in the page settings for the entire page, or within the module setting per module. To have them stacked vertically all you need to do is add 2 modules to the same pane, but to get thm stacked horizontally, you'll need two panes that are next to each other.
I'm not sure about the Out of Memory question, it might be something to do with your server, or maybe not. Hopefully someone else will know the answer to this.
Hope this helps,