Showing side-by-side comparison of individual lines of SQL code is not exposed in SQL Compare's API.
You could use the command-line version of SQL Compare to generate a report - the "interactive" report format will compare lines of SQL and show the results, broken down by object, in a web browser.
There is a code sample for generating a similar report using the SDK, but it's probably not as good as using the command-line version of the commercial SQL Compare.
http://sdk.red-gate.com/index.php/Repor ... ifferences
Hopefully this helps.