It depends slightly on your company structure. In my case, as a sole proprietorship, all contributions, including employer contributions, go on 1040 line 28. This is the line where most people record their own salary deferrals to any 401(k). That is to say, with a sole proprietorship, you lump the entire amount contributed in one line, when prompted about normal 401(k) contributions.
With an S-Corp, since the employer contribution then becomes a business expense instead of a personal income deduction, the individual contribution goes on line 28, and the corporate profit sharing goes in the filing for the corp.
I use Deluxe Turbotax, the online version. It took me a little bit to get it figured out as well.