In account settings ,Account Activation mail settings is general i think so.
I want the account activation mail to be altered. I want to check roles, according to that display the mail messages .
how will i do that?
You can create a new rule like this
After saving a new user account
Conditions saying User has role(s) check your role there.
send mail you can send the mail what you want in that.
You should look into the hook_mail_alter for overriding the mail, which get send after user_save. You can look into the answer given for this question here --
Though question is not relevant but the answer is.