Ford owns only a few % of Mazda now. I think it used to be 30%. The new Ford Fusion and Mazda 6 are completely different cars now. The Fusion will still use the base 2.5 Duratec which is essentially an 2.5 MZR rebadged. The two other engines from Ford will be the 1.6 ecoboost and 2.0 ecoboost. It shares more parts (and looks) with the European Ford Mondeo than it did with the old Fusion. This new Fusion will now be a "global car" meaning the car won't change much from one country to another.
For the Mazda 6, its an all new frame, motor and transmission. It will share nothing with the Fusion. I haven't heard of the engine choice, but I'm guessing a new 2.5 Skyactiv with 6-speed Manual and Auto and probably a V6 from another company. I heard Volvo is looking for a small partner to share some costs. This would be a nice opportunity for Mazda to get some nice Inline-6 engines in their line-up. The design looks somewhat different IMO, but I can see some similarities.