Im hardly qualified but at least let me try and see if I can help you here..You asked what Jude was referring to when he was talking about praying in the Holy Ghost, I think he meant that we are to continue to ask the Holy Ghost for help when we are in need.
Jude 1:17-23 (King James Version)
17But, beloved, remember ye the words which were spoken before of the apostles of our Lord Jesus Christ;
18How that they told you there should be mockers in the last time, who should walk after their own ungodly lusts.
19These be they who separate themselves, sensual, having not the Spirit.
20But ye, beloved, building up yourselves on your most holy faith, praying in the Holy Ghost,
21Keep yourselves in the love of God, looking for the mercy of our Lord Jesus Christ unto eternal life.
22And of some have compassion, making a difference:
23And others save with fear, pulling them out of the fire; hating even the garment spotted by the flesh.
Jude 1:17-23 (Amplified Bible)
17But you must remember, beloved, the predictions which were made by the apostles (the special messengers) of our Lord Jesus Christ (the Messiah, the Anointed One).
18They told you beforehand, In the last days (in the end time) there will be scoffers [who seek to gratify their own unholy desires], following after their own ungodly passions.
19It is these who are [agitators] setting up distinctions and causing divisions--merely sensual [creatures, carnal, worldly-minded people], devoid of the [Holy] Spirit and destitute of any higher spiritual life.
20But you, beloved, build yourselves up [founded] on your most holy faith [[a]make progress, rise like an edifice higher and higher], praying in the Holy Spirit;
21Guard and keep yourselves in the love of God; expect and patiently wait for the mercy of our Lord Jesus Christ (the Messiah)--[which will bring you] unto life eternal.
22And refute [so as to] convict some who dispute with you, and on some have mercy who waver and doubt.
23[Strive to] save others, snatching [them] out of [the] fire; on others take pity [but] with fear, loathing even the garment spotted by the flesh and polluted by their sensuality.(A)
Jude 1:17-23 (The Message)
17-19But remember, dear friends, that the apostles of our Master, Jesus Christ, told us this would happen: "In the last days there will be people who don't take these things seriously anymore. They'll treat them like a joke, and make a religion of their own whims and lusts." These are the ones who split churches, thinking only of themselves. There's nothing to them, no sign of the Spirit!
20-21But you, dear friends, carefully build yourselves up in this most holy faith by praying in the Holy Spirit, staying right at the center of God's love, keeping your arms open and outstretched, ready for the mercy of our Master, Jesus Christ. This is the unending life, the real life!
22-23Go easy on those who hesitate in the faith. Go after those who take the wrong way. Be tender with sinners, but not soft on sin. The sin itself stinks to high heaven.
The Holy Spirit's desire and purpose is to help you -- not to hinder you.
So we need to ask the holy spirit for help in everything we do because it guides us, helps us in our weakness, sancifiies us, and etc and when you are in need of help, the Holy Spirit comes to help you and get you back on your feet. It helps you from stumbling, convicts you of sin, helps turn you away from sin.
I hope the scriptures from various bibles helps answer ur question?
So maybe the part in Judas is referring that when we stumble, we should pray and call on to the Holy Ghost to help us and he will.
Lacey