Hi,
You don't need to edit directly the core file as Xavier said.
You can actually do that change directly in the custom_fields_boostrap view file as an override.
Just change the code :
echo $this->fieldsClass->display(
			$oneExtraField,
			@$this->$type->$fieldName,
			'data['.$type.']['.$fieldName.']',
			false,
			' '.$onWhat.'="hikashopToggleFields(this.value,\''.$fieldName.'\',\''.$type.'\',0);"',
			false,
			$this->extraFields[$type],
			$this->$type
	);
to:
echo str_replace('inputbox','form-control', $this->fieldsClass->display(
			$oneExtraField,
			@$this->$type->$fieldName,
			'data['.$type.']['.$fieldName.']',
			false,
			' '.$onWhat.'="hikashopToggleFields(this.value,\''.$fieldName.'\',\''.$type.'\',0);"',
			false,
			$this->extraFields[$type],
			$this->$type)
	);