How to output signal though SMA connector in Spartan 3E Starter Kit
There is only one Spartan 3E Starter Kit Board.  The PDF is below.
http://www.xilinx.com/support/documentation/boards_and_kits/ug230.pdf

From the PDF:

"The SMA connector allows an external clock source to drive one of the FPGA’s global clock
inputs. Alternatively, the FPGA can provide a high-performance clock to another board via
the SMA connector. See Chapter 3, “Clock Sources,” for additional information."



NET "CLK_50MHZ" LOC = "C9" | IOSTANDARD = LVCMOS33 ;
NET "CLK_SMA" LOC = "A10" | IOSTANDARD = LVCMOS33 ;
NET "CLK_SMA" LOC = "A10" | IOSTANDARD = LVCMOS33 ;


Figure 3-2: UCF Location Constraints for Clock Sources



The UCF file is how you set a signal to a pin.  Is this the info you're missing?