Calibre allows you to save your default setup. In your .csrch file, set:
setenv MGC_CALIBRE_DRC_RUNSET_FILE ./.calibre.drc
setenv MGC_CALIBRE_LVS_RUNSET_FILE ./.calibre.lvs
setenv MGC_CALIBRE_PEX_RUNSET_FILE ./.calibre.rcx
In Calibre, setup things the way you like it. Then save your calibre runset as the above filenames and your rules file and Calibre options (ex, multithreading, etc.) will load automagically.