When using Ice and Water Shield on your roof you should normally use the felt roofing paper on the entire roof and then put the Ice and Water Shield along the eves of the roof which is what I was told to do by a friend that is a roofer.
However I have seen some people putting the felt over the ice and water shield but I believe that is wrong and according to my roofer friend it is and he's been doing roofing for 20 years now.
But you could put Ice and Water Shield over the entire roof and then lay the roofing felt over it which really won't do any harm but will just cost you more money but will protect your roof more.
My friend is a pro roofer and does quality jobs so he does what he needs to do to get a pro job done but as a DIY person doing it for your own self then there really is no wrong way of doing the ice and water shield and overdoing it is okay.
But if you just apply the ice and water shield at the eves of the roof then the roofing felt should go under the Ice and Water Shield.