There is a graphical program to show you your current HAL set up. Its called halshow.
if your using AXIS you find it under the machine tab.
Stepconf is used to produce INI and HAL files for a configuration. If you edit the INI or HAL outside of stepconf you will lose these changes next time you use stepconf because stepconf has no idea you changed them.You shouldn't have to edit the INI or HAL file to make the changes you talked about. Only if you are trying to do something unusual / outside the scope of stepconf. If you have some HAL addons you would like there is a file named custom.hal that will not be overwritten by stepconf. This is good for adding jog wheels and pyvcp panels etc.
Stepconf should connect all HAL pins for you and set up the INI file . Then run EMC start halshow and check your inputs and outputs.
did you read this?