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My question is how do i communicate with it?
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At the hardware level, there are wires between the FPGA and the LCD controller. The Embedded Peripherals IP Guide has an Optrex LCD controller core;
http://www.altera.com/literature/ug/ug_embedded_ip.pdf If you add this core to a Qsys system along with a NIOS II processor, then that processor can access the core registers. The address of the registers is determined by you, when you create the Qsys system.
You should be able to open a Qsys example design that came with the kit, open the Qsys system design, and then look at the properties of each component in the Qsys system (select, right-click, and look at the documentation links).
Cheers,
Dave