First of all, read The Community Manual's
emblems page.
Then try this:
Manually edit files Careers.cfg and Careers_0.cfg in folder \My Documents\SH3\data\cfg\Careers\
yourPlayerName\. In both files, change the last occurence of line:
E01=NULL
to:
E01=data/emblems/subemblems/
yourEmblemFile.tga
Try that and let us know if it works.
NOTE: This most probably will NOT take effect right away, if you're in mid-patrol in your career.