Programming RA6M1 flash with E2Lite

Is there a tutorial somewhere on how to program the RA6M1 flash with E2 lite programmer from e2 studio?  I am currently programming it in debug mode but when the hardware is turned off and on the program does not seem to still be in it.  What settings do I need to do in the e2 studio to make it program the flash and do I need to set the MD pin high or low?  It is currently pulled high.  Thanks.

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