When you enter the Form 1099-R into your return that reports the 401k distribution, there will be a series of follow-up questions. One of those questions will ask what you did with the money. That question is the first step to reporting that it was rolled into an IRA. Be sure to keep going through all the questions until you get back to the main income screen.
Also, you do not report any gains/losses that occur within your IRA account.
