You have a couple of ways to set spatially varying initial conditions.
First, following the user mannual, set key "INITIAL CONDITIONS" be "PARTICULAR", and code "USER_CONDIN_H" or "USER_CONDIN_UV" subroutines. You have to tell the global index of those nodes you want to set with particular values.
Alternatively, pre-run to write out a restart file, and then revise its values using scripts, such as function "alter" of "pretel.manip_telfile", so as to write out a revised restart file in which values are what you need. You may need to revise the scripts to be able to do the revision.