If you use the Lucid Virtu MVP (the latest version of Lucid's graphics virtualization hardware), it doesn't matter where you plug your monitors in! :D
You can plug one of them into the motherboard and one into the discrete, or both into the discrete, or both into the motherboard.
There are slight technical differences in the way things get handled if you plug them in irregularly, but the bottom line is that you'll be able to use both monitors and both GPUs will be helping out with the rendering when you play games in Hybrid Graphics mode. And Yes you can use "Extended Desktop" feature where your Windows desktop is extended seamlessly across both monitors and you can drag and drop windows across, or have a window straddling both monitors at the same time (although this is very slow if you do this during regular operation; long term it's recommended to keep each window on only one monitor).
I don't know that all Z77 motherboards will support this, but if the product material says it supports a Lucid Virtu MVP, you're good.
NOTE: If your discrete GPU is faster than the HD4000 graphics on the processor (very likely, although I don't know just how stripped-down a GeForce GT240 is; it may be slower!) then plugging the monitor(s) both directly into the GPU and running in "Discrete" mode is fastest. This mode is technically interesting: 90% of the graphics are rendered by the discrete GPU and are pushed directly to the discrete GPU's video output header, but a portion of the game's Direct3D shaders (and I think OpenGL shaders also) are offloaded to the Intel CPU's HD4000 graphics subsystem. In my experience, this is the fastest possible performance mode if your discrete graphics card is faster than the processor graphics, because there tends to be some latency if you are driving the display on the motherboard and the GPU is processing shaders and having to send them to the motherboard (via the Virtu MVP chip on the mobo) and then to the CPU for the HD4000 graphics to process...
Source: Personal experience. I own an Asus PZ77-V and have tested all possible configurations of the motherboard Lucid Virtu settings as well as the Lucid driver settings and application settings with my Radeon HD7970.