that is the only thing i can think of. you need to follow the default area names, Main etc. verbatim in perhaps case but certainly by name.

$a = new Area('Main');
$a->display($c);

I'm using whatever editable default areas that came with C5.

if you keep the block areas the same name, the content will stay in there. You can see this at work by setting up a demo at:
http://getconcrte5.com/demo and then changing the theme through the design tab on any page.

If you've got something else going on its because your theme is funky, or perhaps there's content in your theme that you thought was managed by cms but is really hard coded?

I moved the graphic to a different block and then added HTML code to put it into a table so that I could add text to the right or left of the picture. I do not see a way to put two blocks side by side one using a picture and then one as a text block within the same row. I suppose there's a way to create such a block but I'm new to Concrete5. I'm used to just hard-coding things in Dreamweaver using HTML and CSS and then publishing what I want. My goal is to setup a new website for a Church and then let them edit their own content but it seems like I'll still have to customize certain webpages as needed. I guess I'll have to read up more on the blocks and customization docs.