The equipment I'm using is
Samsung ht-c5550 home theatre system
Samsung 3d TV
Samsung 3d blu ray player
Sky hd

Have you looked in the manuals with these products yet... most of them have pictures that show you how to hook them up.

I have it set up but I'm not sure how to set up the audio was wondering if anybody knew the correct way of doing it

What specifically about the audio are you having problems with? Did you use HDMI cables (the flat connectors) for everything or the other round ones?

Yes I have the sky box and the 3d player connected to my cinema system via hdmi leads an then to my TV from the cinema system via hdmi I also have an optical lead between them both for audio but I'm only getting the front two speakers working not surround sound

Are you certain the programming actually has the surround sound component to it? Like you are playing a bluray movie where you know it does.

Don't connect your 3D Blu-ray player through your home theater system with HDMI. 3D will not pass-through that unit.

HDMI out from Sky HD into HT system.
HDMI out from HT system to TV.
HDMI out from Blu-ray player into TV.
Fiber optic out from Blu-ray player into HT system.

Disable HDMI-CEC (known on most Samsung equipment as Anynet) as this can cause all kinds of weird issues.

HDMI carries audio and video. So no need to use both. The above is the best method to connect everything, assuming the HT system only has one digital audio connection. According to the specs I looked up it only has one fiber optic connection and no digital coax. Otherwise if it has a second fiber optic or digital coax, then you can use that and connect your Sky HD box directly to your TV just like the Blu-ray player.