Eclipse 3.5 with shell script

Dear experts,

please help me i have eclipse 3.5 Galileo with cdt , when i launch the cdt i get c/c++ options,

my question is i have written my own directory structure for which i want to run my own makefile or shell script,

how to do every time i create makefile in that directory and try to run my inputs it always takes default make of cdt,

how to run my own makefile or my own shell script ,

i tried to run the shell script using the run->external tools->external too configuration

it shows exception occurred while executing the command line,

please help me how to solve this. i am running this on windows with minGw configurations.