One method appears to be using the Supplemental Control File option under Input Files Tab and setting the Control Standard Errors appropriately under Standard Errors Tab.
This limits one to only one file and only one set of SE's ...
I'd like to use a raw file for my control per page 352 of manual:
The simplest and most straight-forward method to define control for a project is to include the control coordinates in a raw data file.
I suck the points into a raw file and set a CSE record of ! ! 0.05 however the vertical reports as FIXED. After some playing around I've discovered that if either N or E are FIXED, then NEZ are FIXED. If Z is FIXED then N and E can have SE's. So in order to get an SE for Z you have to set N and E to some SE (I'm guessing my work around will be setting something down to an RCH to force FIXED without actually saying FIXED)
Examples:
CSE,N !,E !,EL.05,AZ*
Makes...
StErr N: StErr E: StErr Z:
FIXED FIXED FIXED
CSE,N 0.01,E !,EL.05,AZ*
Makes...
StErr N: StErr E: StErr Z:
FIXED FIXED FIXED
CSE,N 0.01,E .01,EL!,AZ*
Makes...
StErr N: StErr E: StErr Z:
0.01 0.01 0.00
I guess 0.00 means "FIXED"
... and finally my work around:
CSE,N .001,E .001,EL.05,AZ*
Makes...
StErr N: StErr E: StErr Z:
0.00 0.00 0.05