Eu sei que este post está desatualizado, mas isso é para alguém que ainda está procurando uma solução:
Estrutura da tabela de presença
id | int
employee_code | varchar
status | enum('check_in','check_out')
created | datetime
Dados
id employee_code status created
1 EMP0001 check_in 2016-08-20 09:30:30
2 EMP0001 check_out 2016-08-20 18:15:00
3 EMP0002 check_in 2016-08-21 14:52:48
4 EMP0002 check_out 2016-08-21 21:09:18
Consulta
SELECT
A1.employee_code,
A1.created AS check_in_at,
A2.created AS check_out_at,
TIMEDIFF(A2.created, A1.created) AS total_time
FROM
tbl_attendances AS A1
INNER JOIN tbl_attendances AS A2
ON A1.employee_code = A2.employee_code
AND DATE(A1.created) = DATE(A2.created)
WHERE 1 = 1
AND A1.status = 'check_in'
AND A2.status = 'check_out'
AND DATE(A1.created) BETWEEN '2016-08-20'
AND '2016-08-21'
AND DATE(A2.created) BETWEEN '2016-08-20'
AND '2016-08-21'
ORDER BY A1.created DESC
Resultados
employee_code check_in_at check_out_at total_time
EMP0002 2016-08-21 14:52:48 2016-08-21 21:09:18 06:16:30
EMP0001 2016-08-20 09:30:30 2016-08-20 18:15:00 08:44:30
Para um funcionário específico, adicione
AND A1.employee_code = 'EMP0001' em WHERE cláusula 
