Spartan 3E FPGA IO & Clock Questions
1) Yes, absolutely.  Most FPGAs can directly route a clock out to a pin.  A slightly better idea is to actually use a DDR flip flop at the pin as the relative timing between this and signals registered in IOB flip flops will be the same.  

2) Nothing in particular.  Just double check that you have them hooked up properly as inputs as the FPGA does not have output drivers on those pins (no, I haven't made that mistake before...)