When configuring a Frame Relay switch layer 1 DCE/DTE is independent of layer 2 DCE/DTE. The "clock rate" command can only be applied on the layer 1 DCE side of the cable. This can be determined by looking at the cable for a DTE/DCE labeling, using the "show controllers serial X/X" command or by just issuing the "clock rate" command on both sides. The side that accepts the command is the layer 1 DCE.
In regards to Frame Relay layer 2 DCE is independent of the layer 1 DCE. Commonly the layer 1 DCE end of the cable is connected to the FRS and the layer 2 DCE is also configured on the FRS side. The configuration of the Frame Relay DCE can be done by using the "frame-relay intf-type dce" command. By default Frame Relay interfaces are DTE. Also as a point of interest the Frame Relay DCE side is the side that commonly generates LMI. I used the word commonly because although unusual you can have a Frame Relay connection without LMI.