You can do it individually on a per-phone basis in the menu, or:
46xxsettings.txt file
## PHY2STAT specifies the speed and duplex settings for the secondary (PC) Ethernet interface.
## Valid values are 0 through 6; the default value is 1.
## Value Operation
## 0 disabled
## 1 auto-negotiate
## 2 10Mbps half-duplex
## 3 10Mbps full-duplex
## 4 100Mbps half-duplex
## 5 100Mbps full-duplex
## 6 1Gbps full-duplex if supported by hardware, otherwise auto-negotiate
## This parameter is supported by:
## 96x1 H.323 R6.0 and later
## 96x1 SIP R6.2 and later (values 1-5 only)
## 96x1 SIP R6.0.x
## 96x0 H.323 R1.0 and later
## 96x0 SIP R1.0 and later
## 46xx H.323 R1.8 and later (values 0-5 only)
## 46xx SIP R2.2 and later (values 0-5 only)
## 16xx H.323 R1.0 and later
## 16CC SIP R1.0 and later
## 1603 SIP R1.0 and later
SET PHY2STAT 0
