Traditional 401k rollover to Roth IRA

My husband rolled hit Traditional 401k over to a Roth IRA. (the investor skipped the middle part where the funds go into a traditional IRA first and then converted to a Roth). My question, is there a way to input this into the online version? What I am getting now is that i have an excess contribution to my IRA which is not the case since this is a rollover. Plus, we have to pay taxes on this "additional" income but my return is not reflecting this. Any ideas or is the only answer to go to a CPA and have them file my taxes?