The Command line on the QuickEdit primary panel (ENDIE110) is hard coded to always be on the top and cannot be changed.
The QE Selection List panel (ENDIE250) and edit panel (ENDIE300) are controlled by the ISPF 0 SETTINGS option.
If after changing the ISPF 0 SETTINGS option for "/ Command line at bottom" , does not reposition the command line on the QE Selection List panel (ENDIE250) and edit panel (ENDIE300) to the bottom of the screen, try deleting the CTL* ISPPROF entities from the user's xxxxx.ISPF.ISPPROF file.