Best Practice is to use auto-negotiation for all device models. However, there are situations where having all 4 ports (the IPS ports and the two link partner's ports) set to auto negotiate may not allow a consistent negotiated speed for both ports in a segment. For example, If a segment is connecting a switch with 10/100/1000 capability to a router with 10/100 capability, the condition can exist whereby the IPS negotiates speed 1000 with the switch but only speed 100 with the router. In this event the switch can deliver much more data than the IPS can pass to the router, given the speed differential negotiated by the IPS with each device. This condition will cause congestion on the IPS given the IPS has limited queuing capability. In order to avoid this condition, the speed and duplex settings of the switch should be manually set to match the highest capability of the router, or 100 full duplex. This will ensure that the port speeds of the IPS for that individual segment are consistent with each other.
NOTE: You cannot hard code Copper Gigabit Ethernet to 1000 on the IPS. Auto negotiation of speed and duplex is a requirement for using 1000 BASE-T according to IEEE standard 802.3-2002.