Video/Audio setup

[amason]

I am new to home theaters and I was wondering if anyone could tell me if I have my setup correct for the best, or close to it, audio and video. I have the Samsung 56" 1080p DLP (HL-S5687W), the Sony BDP-S1 Blu-ray player and have a Yamaha (HTP-5890). I have the player directly connected to the TV using an HDMI cable and the audio connected to the receiver using and fiber cable.

When I am watching movies, I sometimes see grainy parts or something on those lines. For audio, I would think in some parts of the movies, there should be more bass. I have been looking at receivers with HDMI 1.3 and have been thinking about upgrade to all HDMI for video and audio. My questions is, is my setup currently good and I basically getting everything I am going to get and wait a while to upgrade or am I missing out and should look into upgrading. With the upgrade, will I get a lot more performance in video and audio? Any suggestions to improve on my correct setup will me greatly appreciated too. Sorry guys for the long questions. Any help you can give me with help me out a lot. Thanks