In that case, when you save the CSS, prior to trying it on your site, save as plain text.
Then open it in Notepad and copy out only the css, and none of any control characters that FP will lob into the mix.
The process is basically this:
Edit the CSS
Make the changes on your site CSS
See how it looks
and then do it again.
At this stage, editing index.php is not needed, it's just the look that matters, and getting the correct areas in the correct places.
There are only 4 (header / menu / content / footer) so it's not too difficult to achieve.
If you get stuck, feel free to email me - there is a link from my page (click my name).