Yes, you can specify the attributes in the UCF file. For example:
Inst 'Hard_Ethernet_MAC/Hard_Ethernet_MAC/V5HARD_SYS.I_TEMAC/SINGLE_GMII.I_EMAC_TOP/v5_emac_wrapper/v5_emac' EMAC0_PHYINITAUTONEG_ENABLE = TRUE;
You may need to open the design in FPGA Editor or PlanAhead toolto find the instance name.