No worries i found the solution. You need to add a field in the res.company(make it invisible) and make res.config field related to company field(readonly=False) and then  you can configure values in res.config for each company. Record will be unique for each company. Here is the code

in res.company

apply_ded_4 = fields.Integer(string='Apply deduction after',default=4)

apply_ded_4 = fields.Integer(string='Apply deduction after',related="company_id.apply_ded_4",readonly=False,
                             config_parameter='employee_late_check_in.apply_ded_4')

def set_values(self):
    res = super(LateCheckinSettings, self).set_values()
    self.env['ir.config_parameter'].sudo().set_param('apply_ded_4', self.apply_ded_4)
    return res

first_ded = self.company.apply_ded_4

Hope it helps you.