if you cannot access/edit the bashrc you can also manually source the config file each time you start working with StaMPS.
mt_prep_snap is called from the linux command line in order to generate the basic working environment required Some notes on this here: How to prepare Sentinel-1 images stack for PSI/SBAS in SNAP - #1092 by ABraun
you need triangle and snaphu in any case. If you pre-processed the data with SNAP (e.g. like suggested here)
at best, you leave the initial files exported from SNAP in one folder and create a separate working directory for the StaMPS processing (where you first execute mt_prep_snap) as suggested here. The rest of the folder management is done by the StaMPS scripts alone, as long as you don’t move any files or rename directories 
Hope this helps a bit.