"Praying in the Spirit" is not just a catch phrase or a make believe pretense at prayer. Jude mentions it in Jude 1:20. The apostle Paul speaks of it in his spiritual warfare teaching in Ephesians 6:18. We are to live in the Spirit (Galatians 5:25), walk in the Spirit (Galatians 5:16), worship in the Spirit John 4:24) and pray in the Spirit (). John was "in the Spirit" on the Lord's Day while exiled on the Isle of Patmos. (Revelation 1:10) Should not we be as clearly "in the Spirit" when we pray or worship? It is actually possible to be "in the Spirit" when you pray, and contrary, it is possible (lamentably, too often the case) to pray in the flesh and not according to the will of God, or the mind of the Spirit. There is a process by which the believer can enter into a state of waiting and rest in the Holy Spirit in which he can pray that which is on the heart of God. This is what it means to "pray in the Spirit." 
It is entirely possible that you may never have prayed "in the Spirit." Perhaps that is why our prayer meetings are so dull and uninteresting. Much prayer is a recitation of our man made wish-list before God, or it deteriorates into a monologue to God in which others are the primary listeners. This is not praying in the Spirit. This kind of "list praying" is not far from "vain repetitions" and very much like praying a rosary. Too often we pray with prepared lists of requests in our hands. There is a place for the lists as reminders of immediate needs, but too much leaning on the fleshly mind will miss the mind of the Spirit. 
Here are seven steps in preparing our hearts to pray in the Spirit and according to the will of God. Praying in the Spirit does not come automatically. It is the fruit of a fully developed intimacy with God. Learn to know God and you will know the heart of God. 
1. Deal with Sin - (Me) 
David said, "If I regard iniquity in my heart, God will not hear me." Sin hinders our fellowship with God. Sin deafens our ear to the voice of the Spirit. So deal carefully with secret sins of commission and omission Check your heart for sins of Words, Actions, Thoughts, Attitudes, (W.A.T.A.) Confess each to the Lord being specific about it. (Psalm 66:18, Ps 139:23-24, Is 59:1,2, Mt 5:23-24) 
2. Deal with Self & Flesh - (Myself) 
"The spirit is willing, the flesh is weak." Matthew 26:41 (who’s on first? Who is on the throne?) Selfish desires and wants must be laid down. Breathe in the Holy Spirit. Ask for the Holy Spirit to take control of desires. Be in the Spirit, worship in the Spirit and pray in the Spirit. (Romans 8:8, 8:27, James 4:3, Gal 5:16,25)
3. Deal with Thoughts - (I)  
Reign in the wandering mind. His thoughts are not your thoughts. We are instructed to "Bring every thought into the captivity of Christ." (2 Corinthians 10:3-4, Is 26:3, Is 55:8) 
4. Deal with the Devil - (The Enemy) 
He is the hinderer, thief, liar, destroyer, murderer, deceiver (Daniel 9, Zech 3, I Pet 5:9, Rev 12, Eph 6) Resist him steadfastly. Having not dealt with him we are hindered by him. He is allowed to go unchecked, unfettered, un-gagged. "We wrestle not against flesh and blood but principalities and powers." Remember, "Deliver us from evil" is still part of the Lord's prayer. 
5. Agree with God - (Weakness) 
Admit to God that, "We know not how to pray as we ought." Romans 8:26-27, Proverbs 3:5, Luke 22:42 "Nevertheless not my will but thy will be done."  Jesus taught us to pray, "Thy will be done." in the Lord's prayer. (Matthew 6:10)
6. Believe God - (Faith) 
Believe and expect God to lead you by His voice and revelation.  (Rom 8:14)  Believing prayer is acceptable to God. Wishing and hoping are not the same as confident believing prayer. (James 1:6-7, Hebrews 11:6, Romans 4:20) 
7. Wait for God - (Patience) 
Wait on God. Wait patiently for His burden and direction. (Stand Still, be still, keep silence) Psalm 46:10, Psalm 27:14, Ps 37:7, Is 40:31
The Spirit prays for us with groanings that cannot be articulated. (Romans 8:26) If you are never moved to tears when you pray, you are probably not praying the mind of the Spirit. Seek to pray the heart of God – which is the mind of the Spirit. Then continue to pray until the Spirit of God lifts the burden of prayer.