Jack Atlas is significantly harder than most opponents you face until now (the one exception in my mind is Sayer and his psychic deck, though it must be said by pure luck I've yet to face Akiza). He is also significantly better than Yusei. If it's possible for you to beat Yusei first so that you have the Stardust Dragon/multiple copies if you want them, you should definitely do so. Obviously, if you're about to lose, quit to main menu.
Jack himself uses a dragon deck, as you'd expect. He has remarkable luck to draw either future fusion or gold sarcophagus (which he'll use to retrieve future fusion), which he'll use to summon F.G.D (for those who don't know, 5000 attk, 5000 def, only killable in battle by light monsters). Be wary of the possibility of more than one F.G.D, possibly at the same time. Not only can Jack use Dragon's mirror to remove from play the dragons he sends to the grave to summon another one instantly, but even when they're in the grave, Jack is a keen user of Red Eyes Darkness Metal Dragon (2800 attk, special summonable by sacrificing any one dragon, can use its effect to special summon one dragon from his grave or hand per turn), so they can easily come back. This is another move Jack is capable of doing on his first turn, and does so about half the time. I'm fairly sure he has red dragon archfied in his extra deck, but Jack's tendency to focus on his strongest dragons rather than magna drago means that you won't see any syncrhos (I have beaten Jack in 3 matches now and have yet to see a synchro).
A counter deck. This is different to playing in a strictly defensive manner, as eventually, Jack can happily beat down many defenses if not by the fact he's likely to set up 8,000 pts worth of damage before any reasonable shield can be set up, so stock up on bottomless trap hole and any other monster destroyers as odds are you won't be in many battles with your monsters against his. Clearing his back row isn't much of a problem. The spells he uses are future fusion, gold sarcophagus and dragon's mirror as I've previously mentioned, bringing a magic jammer or similar could save yourself a huge 5000 attk problem later. I'm not claiming this to be his only trap, but the only trap he's ever used against me is solemn judgement, which is often a blessing not a curse. Once he uses a solemn judgement, it's very possible to do 4,000 pts in effect damage. Save your magic cylinder for a F.G.D unless it's going to finish you off, and I'd personally advise bringing a lot of the normal monsters you started with and justi-break. Unless you got some amazingly good cards like I did running up to him (namely mirror force and Obelisk the Tormentor), you're going to struggle to kill off his monsters otherwise. Focusing on monster destruction is absolutely crucial as not only are they strong, but they swarm quite well, also. To be honest monster destruction isn't a bad idea for the beginning of the game anyways while you don't have enough cards to make up a real themed deck so this needn't be a pain.
Should you be struggling against Jack, there's no harm in going through single player and losing to Jack just for the cards you get. Best of luck (Y)
EDIT: Undead Immortal has since said that Jack can use mirror force. I myself haven't seen it in 3 matches against him so it's not as common as some of his other cards but it's worth bearing in mind.