Just call the NERDComment function in your mapping. For example, my mapping to comment out the current line:
inoremap ,c <C-o>:call NERDComment(0,"toggle")<C-m>
It describes how this vim file works.
i inoremap , .
noremap , .vimrc .
,c - , .
<C-o> , NERDComment.
:call NERDComment(0,"toggle") - NERDComment.
<C-m> - , .