In short, the indwelling of the Holy Spirit is permanent while the filling of the Holy Spirit is not permanent. A believer can be indwelt but not filled with the Spirit. We do not need to seek the indwelling of the Holy Spirit. God does this to us once and for all the moment we are saved, and we can never lose it. That is why there is no commandment in the Bible to be indwelt, while there is a commandment to be filled or led by the Spirit.
Let us look at some passages of scripture on the indwelling of the Spirit. 1 Corinthians 3:16 – "Know ye not that ye are the temple of God, and that the Spirit of God dwelleth in you?" Romans 8:11 – "But if the Spirit of him that raised up Jesus from the dead dwell in you, he that raised up Christ from the dead shall also quicken your mortal bodies by his Spirit that dwelleth in you." 2 Timothy 1:14 – "That good thing which was committed unto thee keep by the Holy Ghost which dwelleth in us." In all these verses we notice how Paul simply assumes that Christians are indwelt by the Spirit – i.e. it is stated as a fact that is true of all born-again Christians. Romans 8:9 – "But ye are not in the flesh, but in the Spirit, if so be that the Spirit of God dwell in you. Now if any man have not the Spirit of Christ, he is none of his." It is therefore quite clear that every true believer is indwelt with the Spirit of God.
But now look at passages about the filling of the Spirit: Firstly we see that some believers are described as being ‘full of the Holy Spirit’ Acts 6:3 – "Wherefore, brethren, look ye out among you seven men of honest report, full of the Holy Ghost and wisdom, whom we may appoint over this business." Acts 11:24 – "For he [Barnabas] was a good man, and full of the Holy Ghost and of faith: and much people was added unto the Lord." Is this filling only reserved for a special elite group of Christians, who serve the Lord well? No, because the command is given to all in Ephesians 5:18 – "And be not drunk with wine, wherein is excess; but be filled with the Spirit"
Hence the filling of the Spirit is up to us – ideally we should be filled all the time, but it is possible to lose the filling of the spirit because of the old sinful nature in us. This experience is described by Paul himself in Romans 7:19,20 – "For the good that I would I do not: but the evil which I would not, that I do. Now if I do that I would not, it is no more I that do it, but sin that dwelleth in me." Then He mentions how to overcome the flesh, in Romans 8:1,2 – "There is therefore now no condemnation to them which are in Christ Jesus, who walk not after the flesh, but after the Spirit. For the law of the Spirit of life in Christ Jesus hath made me free from the law of sin and death."
The term ‘walking in the Spirit’ implies an ongoing, daily effort of keeping in step with the Holy Spirit. Cf. Galatians 5:16-18 – "This I say then, Walk in the Spirit, and ye shall not fulfil the lust of the flesh. For the flesh lusteth against the Spirit, and the Spirit against the flesh: and these are contrary the one to the other: so that ye cannot do the things that ye would. But if ye be led of the Spirit, ye are not under the law."
Hence it is clear that being filled with the Spirit, is dependent on the believer’s initiative. We must consciously yield ourselves to the Spirit’s leading and working within us.