Yes, there is a setting in the cPanel editor. You can reset your settings by selecting Reset All Interface settings at the bottom of your cPanel screen.
There should be a setting in your FTP client as well to show hidden files.
You can change the permalinks but you have to create an .htaccess file in your WordPress folder and enter the code that WordPress gives you at the bottom of the permalinks page.
That's going to be difficult without a link. But a place to start is did you turn on permalinks in the admin section? If so turn them off and see if you are still getting the error.
You would have to change the files to permissions 666 for the theme manager to write the files. I don't recommend that and don't do it that way myself. I make the changes on my own computer and upload them with an FTP client.
To edit the CSS I recommend using Firefox and the Web Developer Toolbar extension. It allows you to make changes to the CSS and see the results in real time on the server. Then you save the CSS file to your computer and upload it to the theme folder using FTP for everyone else to use.
If you use the FireFTP extension you can even upload it to the server without ever leaving your browser.
Hope that helps.