Deep prayer is not just about learning about God or talking to God. It is about encountering God, deep in your soul. This is the real aim of prayer. It is the difference if giving yourself, rather than just giving things. It is about receiving God, not just things from God. The following is a guide to deep prayer. By the way, another name for deep prayer is contemplation.

Stage 1. Actively seeking God (meditation). You have to work to encounter God. There are many different ways to actively seek God. One is by reading a daily passage from Mark’s gospel, over and over again, slowly thoughtfully. As you meditate upon it and think about it, you start to think about God. As you think about God, you may start to appreciate His goodness, love, kindness, etc. This may lead to the next stage. 

Memorisation as a Method
Often we are distracted during prayer. One way to keep our focus is to memorise the passage we are using for prayer. This means that gradually we are focusing our mental capacities upon the passage and actively thinking about what the passage is really saying to us. We start to discover a depth to our reflection; far deeper than just reading the passage once. As we enter into this depth by memorizing the passage, we become aware of how we are thinking about the passage. Here is a possible mental path we can take during our reflection 
We are trying to memorize, but are distracted. So we keep trying to think and memorize the words. 
Gradually we learn a sentence or two. As we go over these sentences, we start to pick up the rhythm of the passage and reflect in a deeper way upon the passage. 
Particular words stand out and we start to think about them. This is what should be happening. We should stop memorizing and allow ourselves to think about the words and their meaning. For example, When I call, answer me, O God of justice; From anguish you released me, have mercy and hear me!. I may start to think of the words, ˜answer me’. 
I start to personalize the words. The words become my own. I am asking God to, ˜answer me’. I start to pray from the heart and really want God to answer me, now. I become aware of my desire for God and start to desire Him more. 
As this desire deepens, I may become aware of God Himself, being present. This is the next stage of prayer: an awareness of his presence. 
If I become distracted, I need to start again by memorizing the passage and allow myself to go deeper into the passage.

Using a Gospel passage
Imagine the place where the meditation is set. First recall what took place in the passage using your memory then as you think about it reflect on various aspects of the passage, why did things happen as they did, then connect your emotions with what Jesus was feeling, and allow yourself to respond emotionally to the passage, to feel Christ’s compassion, or to be aware of how you could better live the way Jesus lived. Talk with Christ about the passage as one friend speaks to another, eg ask for some grace, or blame yourself for some misdeed, or talk about what is happening in your life or asking for God’s guidance in your life. During all of these steps the aim is to be open to God's presence with you.

Stage 2. Awareness of God’s presence. Have you ever had the experience of feeling as if someone is looking at you, then turning and seeing the person looking at you? Some do. This is a bit like that inner awareness of God’s presence, except, God always looks on us with eyes of love. As I become aware of His presence in my soul, it is like I know where He is. He is with me, right now, really present. His presence is a presence of love. I begin to cross over from my work to letting God work in me. I should give over to God’s presence, and decrease the work to let God increase His work in me. I should stop memorizing and give myself over to God. This is the next stage: contemplation.

Stage 3. Surrender (Contemplation). Once you are aware of God’s presence, you can surrender yourself to that presence. It is just a matter of giving yourself to God and enjoying the deepening embrace of His love. St. Teresa of Avila calls this the prayer of quiet. This is the proper spiritual meaning of contemplation. Gradually we let God have more and more of me. The aim of prayer, therefore, is surrender: to let God be God; to receive His grace and love. 
As our experience of personal prayer deepens, it increases the experience of prayer at other times when we pray. We experience God’s love personally in a real and direct way.

You need to be aware of a couple of things when it comes to deep prayer. If you are starting to experience a higher form of prayer, give over to it, eg if using the memorising method and you start to actually reflect upon the words and you are gaining insight into their deeper meaning, then allow yourself to focus on this reflection and stop memorising. If you become distracted, start with actively seeking God again, ie if while you are reflecting, you become distracted and think about something else, start memorising again. If it is a scripture based prayer, then initially it is just reading scripture, then beginning to imagine the scene, then focussing on what is happening, then focussing on Jesus, then focussing on what he is thinking, then focusing on his feelings and seeking to become one with his heart. It could be that you reflect on other aspects which is fine as long as it is leading you deeper towards God. The next stage is becoming aware that God himself is with you and truly present and surrendering to that presence. At times we should stop the prayer method and focus on God's presence at other times we can keep the rythmn of prayer (such as the rosary) to take us deeper into God's presence.
Any prayer method can be the basis for deeper prayer. Deeper prayer is about being open to the presence of the Holy Spirit and responding to his presence.

Consolation/Desolation

As we experience God’s presence, which we call consolation, we may also experience the opposite: desolation. Spiritual writers use these two words to describe positive and negative spiritual experiences. When experiencing the warmth of God’s love, this is called consolation. It is like the warm embrace of a parent, or friend. That inner warmth, that you are loved as you are that brings joy and happiness. The opposite is desolation. This is a feeling of absence of God’s love. It is horrible. You feel blah, like you are the worst. Abandoned, inner agony and pain. You feel like, What have I done wrong? Jesus experienced desolation in the garden of Gethsemane. St Ignatius writes about these experiences. He says that the experience is not the important thing, but what you do about it is. God still loves you just as much in consolation as in desolation, but allows you to grow in more love of Him, through them. It is easy to pray in consolation, but we really grow in love, by continuing to pray in desolation. Even if you don’t experience anything, your love of God grows and the graces he gives you increases by continuing to pray even if you don’t feel like it. The bottom line is to keep praying. As St. Ignatius suggests, increase prayer a little even when it is hard. We will learn more about consolation and desolation when we talk about discernment.