What I'm doing here is getting the reservations and the user which are duplicate. Here reservation ticket can not be printed twice. If a user prints a ticket tracker table updates with that record. If a user prints the same ticket twice it's marked as a duplicate. What subquery does here is return some reservation ids which are marked as duplicates.
SELECT t1.id AS res_id,
t1.tx_id,
t1.tx_date,
t1.bx_date,
t1.method,
t1.theater_id,
t1.showtime_id,
t1.category_id,
t1.amount,
t1.fname,
t1.status,
t1.mobile,
u.username,
t2.*
FROM `reservation` AS t1
INNER JOIN
( SELECT *
FROM `tracker`
WHERE reservation_id IN
( SELECT reservation_id
FROM `tracker`
GROUP BY reservation_id HAVING ( METHOD = 1
AND TYPE = 0
AND COUNT(*) > 1 )
OR ( METHOD = 1
AND TYPE = 1
AND COUNT(*) > 1 )
OR ( METHOD = 2
AND TYPE = 2
AND COUNT(*) > 0 )
OR ( METHOD = 3
AND TYPE = 0
AND COUNT(*) > 0 )
OR ( METHOD = 3
AND TYPE = 1
AND COUNT(*) > 1 )
OR ( METHOD = 3
AND TYPE = 3
AND COUNT(*) > 0 )) ) AS t2 ON t1.id = t2.reservation_id
INNER JOIN `users` AS u ON u.id = t2.user_id
WHERE t2.resolved = 0
AND t2.duplicate = 1
ORDER BY t2.issue_date DESC, t1.id DESC
EXPLAIN Command of the above query.

What should I do? If I'm index which keys should I use? How can I decide which keys to index? I know subquery slows me down What procedures should I follow to eliminate the slowness?
In MySQL, exists subqueries are often faster than in subqueries. You might try:
SELECT t1.id AS res_id, t1.tx_id, t1.tx_date, t1.bx_date,t1.method, t1.theater_id, t1.showtime_id,
t1.category_id, t1.amount, t1.fname, t1.status, t1.mobile, u.username, t2.*
FROM `reservation` t1 INNER JOIN
(SELECT *
FROM `tracker` t
WHERE EXISTS (SELECT 1
FROM `tracker` t3
where t3.reservation_id = t.reservation_id
GROUP BY reservation_id
HAVING (METHOD = 1 AND TYPE = 0 AND COUNT(*) > 1) OR
(METHOD = 1 AND TYPE = 1 AND COUNT(*) > 1) OR
(METHOD = 2 AND TYPE = 2 AND COUNT(*) > 0) OR
(METHOD = 3 AND TYPE = 0 AND COUNT(*) > 0) OR
(METHOD = 3 AND TYPE = 1 AND COUNT(*) > 1) OR
(METHOD = 3 AND TYPE = 3 AND COUNT(*) > 0)
)
) t2
ON t1.id = t2.reservation_id INNER JOIN
`users` AS u ON u.id = t2.user_id
WHERE t2.resolved = 0 AND t2.duplicate = 1
ORDER BY t2.issue_date DESC, t1.id DESC
I notice the subquery is using Hidden Columns in the having clause. It may not be doing what you expect. Normally, the query would include method and type in the group by clause or have an expression such as max(Method).
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