for simplicities sake i'll try to break this up into sections....
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i am not sure why you mentioned optical (perhaps because the z906 has it??). the only thing which needs to be able to handle the transfer of the digital signal is anything between your source and the DAC (digital analog converter). the source is the program reading the disk (lets just say your motherboard is the source) and the DAC is the soundcard (a soundcard is essentially a dac, amp with a few other electronics on it).
it exports an analog signal to the speakers which causes them to fire. the 3.5mm connections do not need to handle any special formats as they are after the DAC unit and are just transmitting the electrical signal to drive the speakers.
now where does optical come in? if you bypassed your soundcard and were exporting the information via optical to be used on either an external dac+amp, receiver or speaker with an internal soundcard. optical only supports uncompressed sound in stereo (2.0) and for surround needs to use dolby digital live (DDL) format. honestly hooking up via optical would only be good if your onboard sound is bad.
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now, what you say about not all soundcards handling all formats is true. however... do realize that if you have a $50 soundcard and $100 speakers then it doesnt really matter if the soundcard is only decoding a DD signal instead of DTS or DTS-HD as you likely will not hear much of a difference anyways. if you had $400 speakers and a $50 soundcard then you probably would. pairing a $250 soundcard with a $300 computer speaker set is also pretty outlandish.
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yes it looks like you have a pci x1 slot so that soundcard would work. there are likely better options than going that route though.
afaik the z906 has optical, coax and 3.5mm inputs. i just looked at the specs and see nothing about hdmi.
in any case if it did have hdmi all you would be doing with that $250 soundcard is completely bypassing it and using it as a way to pass data through on hdmi. basically you might as well light a few fifties on fire and dance around in a circle. now, if you hooked the z906 up via 3.5mm to that soundcard then yes there is a point to the purchase and it will sound better than on a cheap soundcard. while i dont agree that its really required for just computer speakers (regardless of how well rated they are) you might actually hear a difference.
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by raw i'm guessing you mean "full quality" and no, none of what you mentioned so far is really an ideal way to do this.
now if you used a soundcard which supported DTS-HD or other lossless formats and hooked up pc speakers to it via 3.5mm cables then yes. however... on pc speakers would you even be able to hear the difference between that and good compressed (or other format) sound? unless you are an audiophile that answer would be no.
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i've never heard of totalmedia theatre. i've used powerdvd though and while not perfect its pretty decent.
it sounds like you are trying to spend a whole lot of money just to get "raw" sound as you put it. for the money you are thinking about putting out you could likely do better in sound quality than what you mentioned earlier (a receiver and speaker set would be better) or you could likely not even hear the difference when using a half decent soundcard and pc speakers. honestly it all depends if you're an audiophile.
generally the dac/amp part of a home theater system set should be about 25-33% of the cost of your entire system. for my own system i used a $500 receiver paired with $550 speakers and a $350 sub. i spent about 35% on my own however i really wanted the nice on screen display (which was only one the elite models at the time) and a few of the other features so i bought something a bit over what i actually needed.
now, while the same figures dont really hold true to pc speakers its similar. you wouldnt buy a $250 soundcard for $300 speakers unless you were a complete audiophile and absolutely needed perfect sound (which why are you buying pc speakers anyways if that is the case?). at most i would say a $100-150 soundcard (when paired with a z906 thats about $450 total). when the budget starts getting too high you start to encroach on territory which is better handled by the home theater market..
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what is a receiver?
well if you want to see some photos of a setup you can see mine which is in my signature link. posted here for easy navigation: http
/postimg.org/gallery/ql0xj0nu/
basically a receiver is a digital analog converter (DAC), an amplifier (AMP), a tuner (AM/FM radio), a switch (to swap between inputs), an equalizer (EQ) and some other electronics all packed into one box. a more simplistic explanation is that it allows you to attach multiple devices (pc, consoles, ipod, etc) and play them through the same sound system.
one nice benefit is that they take direct hdmi inputs (from your video card) and typically handle most formats of sound. from the pc you will get pulse channel modulation (PCM) sound which is pretty as perfect as sound is going to be. think of this as the "raw" sound you were talking about. there is no need for any special soundcards when going through hdmi.
i dont adjust volume on the pc typically. i just turn it down on the receiver. i also dont use any special equalizer settings i just change the receiver settings. to swap between inputs i just turn one knob. it really is quite handy.
now you dont really technically need a receiver but its more convenient for 5.1 sound. for 2.0 or 2.1 you could just use a soundcard and have some bookshelf speakers hooked up. technically you could just run multiple stereo 2.0 amps, one for each 2 speakers and connect it all up to a 5.1 soundcard but thats alot of wires and a bit messy. a receiver is more compact and not bad on price for what you get.
half decent 5.1 receiver costs start at about $200 for the basics. the lowest cost speaker set i can recommend off the top of my head is the energy take 5.1 classic at $350. thats about $500 and gets you into the world of true home theater.
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as far as how are the z5500/z906 compared to the energy take classic 5.1 and a receiver?
better sound out of the energies and likely louder too. you dont need to go out and buy a soundcard but can use what you already have if you got a receiver. if you wanted to hook up other sources like a console, roku or other device its better/easier on a receiver.
the z906 is a bit cheaper though (not if you buy a soundcard!), doesnt require a receiver box (though it does have a control unit), and is a bit less complicated to set up.
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my recommendations? well i'll hold off on that until you give a response to what i've said above.