Hometheater speakers to receiver?

Hi, I have a Sony STRDH720 7.1 Channel 3D AV Receiver and when I connect my Iphone through 3.5mm jack to RCA in the back of receiver sound only plays through couple of the speakers. I have a 5.1 set up.two front, two back, center and a subwoofer speakers. So this is the first problem I run into when I connect something to play through the RCA connection I don't hear sound through all speakers.
second problem is that I don't hear the subwoofer. I have to go and change the front speaker size to "small" only then I can hear the sub.
can you guys give me some advices on what i'm doing wrong.
here is the SUB i have Yamaha YST-SW216BL Subwoofer
and the speakers i use are from this set, sony hcd fx500

You should be able to but the subwoofers just need turning up

You're connecting a 2-ch source so you're not going to get sound through all speakers unless your receiver has some sort of "All Channel Stereo" mode. It might be called something else on your receiver, look through the surround mode menu and find something that will turn your 2-ch input into all channel mode.

As for why the sub only plays when in small speaker mode, you probably have the sub setup menu set to off. It defaults to on when in small speaker mode but reverts to off when in large speaker mode. Generally there's no reason for you not to run in small speaker mode anyway unless your main speakers are large enough to support the bass. You probably should leave it in small speaker mode.

Change your speaker size to "Small" permanently. If you want stereo sources to play through all speakers, change the soundfield to "MULTI ST". READ THE MANUAL.

OK so here is your issue

1) you are connecting your ipod into a stereo Source (2 cable rca Red/white) so you won't get surround sound unless you have a simulated surround sound field on your receiver.

2) unless you set your front speakers to small your receiver won't output bass to the sub, it will send it to the front speakers. I have 2 floor standing speakers with a freq range of 36Hz to 22 kHz and I set mine to small. However I can set my receiver to output bass to both sub and front speakers. I just use the cross over to 60 Hz so the sub will take over at that point. I added a link about small/large setup It's a good read

You are connect a 2 channel stereo device to the receiver and you want 5.1 audio. It is not going to happen. Keep in mind that surround sound are only available from DVD, Blu Ray and some video games. Some receiver will have a sound setting to all stereo. Hope this will help you out.