I don't have Nero 6, so if you have that version, I will say no. Maybe someone that has it will know for sure. There may be an add on you can get, but I don't know if Nero Digital will work with Nero 6. If you have Nero 7, do you have Nero Recode 2? If not, you could upgrade to Nero 7 or get just the Nero Digital, it does have a 30 day trial. http://www.nero.com/nero7/enu/Nero_Recode_2.html
This guide, not using Nero may help you http://www.afterdawn.com/guides/archive/convert_video_to_mp4_for_ipod_guide.cfm there are more guides available by clicking on guide tabs at the top of the page.