Not sure I understand the question now.

Keep the *.inc files as Pic Basic will look for it even if it is not being used.

Most of the time I set the *.inc file the way I want the configuration to be. Others like to do it in their code.

If you set the config in code the lines in the *.inc need to be commented (rem) out, if not you will get errors.

If I understand when you were using the*.inc file nothing happened. There may be another setting in that file that was causing the problem. ??? How is MCLR set in the *.inc?