Pre/Pro question.....

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All,
So I had been using my pioneer elite vsx-94txh as a pre for a few years paired with a B&K AV5000 series II amplifier. I have always wanted to get into separates so when the Marantz AV7005 came up for sale locally (thanks Paul) I jumped on it. I am trying to navigate through the set-up and optimize picture and sound. Blu Ray looks and sounds amazing. Roku works great. However, there is something off about my television and FIOS.....the sound and picture seem compressed is the best way I can explain it. My cable box is set to HD/1080i. What setting should I set for the Pre in the SAT setting? Basically, I guess what I am asking is, should I let the set top box decode or allow the pre to decode the signals. If so, how would I go about optimizing each so that the picture and sound is best? If there is any other information necessary to help answer I am happy to provide. I have it set to AUTO now thinking that would "upscale" to the best format, but the picture seems off in color and definition. Didn't look this way with the Pio elite......any suggestions are greatly appreciated and thanks in advance.
Shawn
AVR: Marantz SR-5011
Center Channel: Polk LsiM706c
Front: Polk LsiM703
Rear: LSI fx
Subwoofer: SVS 20-39pci
Television: Samsung UN58NU7100FXZA
DVD Player: Sony PS4