Section 45.4.10.3 of the Reference Manual (IMX53RM) discusses how LCD clock signals are generated.
Basically, you have to define the clock signal in the software driver and assign it to one of eight available counters (Counter #9 is special, and does not get defined indepently). These counters are labeled DIx_PINy where x is the DI interface used (0,1) and y is the counter # (1-8). The BSP provided by Freescale, for example, already defines the HSYNC signal under counter DI0_PIN2.
To ouput these signals, you need to select the appropriate IOMUX pin option to output the defined counter. For example DI0_PIN2 is the ALT0 option for pin DI0_PIN2, while counter DI0-PIN7 is the ALT2 mux option for pin EIM_D18.
Chapter 4 of the Reference Manual maps out the Available pin muxing options and Chapter 43 contains all the register definitions to define mux assignments.
So, yes you can assign HSYNCH to any DI#_PIN# in the driver, and then select the appropriate mux pin option for the new pin you wish to use.