New answers tagged chipset
You should plug both monitors into the graphics card, as your graphics card is substantially more powerful than the built-in GPU. If they are displaying the same image, this takes almost no additional processing power. It's not remotely clear this is your intention, though, as you say you want to use the monitors for different things. If you aren't ...
The AMD SB950 Southbridge does appear to support Port Multiplication. Be sure that if your motherboard has more than one IO controller (like the ASMedia controller), that you are using the SB950 sata ports for muxing, rather than any others which may or may not support PMP (this goes for controllers from Marvel, Intel RST, JMicron, etc as well).
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