The theme options would be carried over automatically because they're saved in the WP database, and as long as you don't click the "Reset ALL theme options" button they won't be deleted when you upload a new theme version.
But any manual theme edits you may have made you would have to (manually) re-apply to the new files.
The update from 3.1.7 to 3.1.8/3.1.9 had a rather major change regarding the placement of the dynamic CSS. Since the CSS is now inline inside header.php, any image references (i.e. CSS background images) you may have made would have to be changed to absolute paths
would have to be changed to new:
That should be all