As a rollover it's not considered a contribution of new money. If the money was moved trustee-to-trustee and the money was never paid to you, you should not receive a Form 1099-R. A trustee-to-trustee transfer from your SEP-IRA to another traditional IRA is neither a distribution nor a rollover and is not reportable.
However, if the money was paid to you and you rolled the money over yourself within 60 days, yes, you should have received a Form 1099-R. Enter the 1099-R and say that it was rolled over. A SEP-IRA is a type of traditional IRA. If asked, select traditional IRA.
When your employer uses an SEP plan instead, only your employer can make contributions to your IRA account. This is opposed to a SIMPLE IRA where your employer can withhold contributions directly from each of your paychecks on a pretax basis, meaning income taxes are calculated on your W-2 salary only after reductions for your contributions.
