Bismillahir Rahmanir Rahim,
Let’s take a look at some general principles regarding the names of Allah (taken from the book Explanation to the Beautiful and Perfect Names of Allah by Shaykh as-Sa’di):
The names of Allah can only be known through revelation.
We can’t perceive the unseen. It is only Allah who can inform us about Himself. In fact, this is one of the major areas in which the deviant sects of Islam and even other religions went astray. They attributed to Allah what they felt that were His attributes, without any reference to revelation. For example, the Christians believe that Allah is a father, i.e. that He has a son.
Say, “My Lord has only forbidden immoralities – what is apparent of them and what is concealed – and sin, and oppression without right, and that you associate with Allah that for which He has not sent down authority, and that you say about Allah that which you do not know.” [Quran, 7:33]
The Names of Allah are not limited to ninety-nine, or any other number. In a dua the Prophet said:
I ask You by every name belonging to You which You named Yourself with, or revealed in Your Book, or You taught to any of Your creation, or You have preserved in the knowledge of the unseen with You . . . [Ahmad]
Also, in the Quran alone there are more names mentioned than ninety nine.
All of Allah’s names are beautiful and perfect.
When we say subhanallah, we are declaring Allah’s perfection and denying the attribution of any defect to Him. Every name that belongs to Allah is perfect, every attribute of Allah is perfect. All His actions are perfect and beneficial for us, even if it is taking something away from us that we love.
The names are proper names and descriptions.
The author says that the names of Allah are proper names, “‘with respect to their referring to the Essence or Person of Allah and descriptions with respect to the meanings they carry.” 
Thus, when Allah says He is ar-Rahman, the Most Merciful, it means that He possesses the quality of mercy. When He is called al-Aleem, the All-Knowing, it means He possesses knowledge of everything.
If a name points to a description that is transitive (i.e. it takes an object), three things have to be acknowledged and affirmed by us:
a. That particular name
b. The attribute which the name indicates
c. The ruling and implications necessarily contained in it
There are many instances in the Quran where Allah gives a certain point and at the end of the verse or the passage mentions one or two of His names. These specific names are mentioned for a purpose and are related to the subject matter of the verse.
For example, Allah mentions the punishment of highway robbers in verse 5:33. After that He says, ‘Except for those who return [repenting] before you apprehend them. And know that Allah is Forgiving and Merciful.’ [5:34]
The fact that Allah is Forgiving and Merciful is affirmed by taking off punishment from the robbers.
If a name is not transitive then only the first two need to be affirmed. For example, when Allah says He is al-Jameel, the Beautiful, we need to affirm that He is the possessor of that name, and also that He has the attribute of beauty.
Learn Tajweed real easy: here’s a free lesson. Try it out!