I had similar problems. Being quite new to WordPress, I thought I'd search for a theme closest to the layout I had in mind, and work on customising that one.
After a little searching, I came across a theme called 'Loved' on Mozspot. It was nice and simple, and I could easily navigate and understand the stylesheet.
My problem arose when I wanted to change the footer. I opened the file to see lots of encrypted crap and another folder called 'scopbin' which contained a php file of similar construct. At first I thought this was the same with all wordpress themes (being new to it) and so wanted to find the maker of the Loved theme to ask how I go about changing the footer code.
Thankfully though, I had the sense to look at the footer coding of some other themes and realised this coding style was not the norm.
Having XAMPP on my desktop helped. I ran the theme and wordpress there to try things out... At first I imported a new footer.php from another theme as a test. The result: No sidebar. The site just crashed.
So... I thought "This sucks!" I spent two days getting the layout, images, sidebar, and even incorporated a double border for what? For nothing. I was just unlucky in my selection of an existing theme to work from.
Next I tried to import the css file, together with the images, into a copy of the default theme which I renamed 'Forest' (I'd decided to call my theme Forest)
Then I imported over sidebar.php and index.php. Added an extra div tag in index.php and single.php to call up the second background, editied footer.php and it worked!
My problem now is that not everything is going as smooth as it should, perhaps, have done. But at least I'm slowly ironing out the creases. Next time I'm going to build a theme and stylesheet from scratch.
Twilight