I’m new to D&D and have only ever played a couple sessions. I have played about 300 hours of Baldur’s Gate 3, so I impulsively picked Descent into Avernus to run with youth I support at work and a group of my friends. Both groups are up to the Dungeon of the Dead Three and are having a great time.

I didn’t read the whole campaign or read about the issues it has before I started. I’m now wondering if I should have picked something more geared towards a beginner DM, as it seems like I might have to mod it a lot to make it work smoothly.

Should I keep running it or start something easier? 

I admit to having no idea what the supposed problems with it are. (Never read the adventure.)

However, since people are having fun, I'd be reluctant to pull the plug in the middle.

Read ahead, think about whether the supposed problems will actually be problems with your groups (for instance, if it forces the players into a specific set of choices, that's often not a problem with new players), and spend some time thinking about how to shore the adventure up before you get there.

IMO, making stuff up to react to what the players are doing is one of the more fun parts of DMing, and, while you may be getting thrown into the deep end sooner than is ideal, at least you have the scaffolding of the adventure to build upon.

You'll do fine.You'll make mistakes, but as long as everyone, including you, is having fun, they don't really matter.

I would attempt to wrap things up in a way that makes sense, but you are well within your rights to tell the group you bit off more than you can chew.

Switching to something new might also be a convenient time to move a couple of your players into the DM's role.

I can recommend Dragon of Icespire Peak as a good intro to DM'ing. It's a little rough in some parts,

 but if you have 3 players instead of 6, you can manually tweak some of those things.

Keep running it. You're the only one that ever knows "what you should have done." As long as they're having fun, your players just think you're doing a good job. If it were not so, they'd tell you. 

Forget what the internet tells you. You don't have to mod anything unless your players are having too much trouble with (or just breezing through) the fights. As far as their reasons to go save Elturiel.. well, if they don't stop it, Baldur's Gate is going down too and they're going with it. 

Read ahead in the adventure.  A problem in the trajectory, I feel is that if your party isn't 100% noble-minded they may be very much "the hell with Elturel, literally" and have no interest in pushing the adventure beyond The Dungeon of the Dead Three   Vanthampur Villa.

There are a lot of options after completing the Dungeon of the Dead Three raid on Vanthampur Villa for a DM who knows his players don't want to go to Hell to save an innocent city of sanctimonious goody two shoes.  They could deliver word of their findings to Candlekeep, but rather than progressing into the Descent into Avernus proper, you could try out a couple of the adventures from Candlekeep Mysteries, an anthology based out of Candlekeep but sends characters on a number of pretty good investigation-geared adventures.  If you prefer to stay in Baldur's Gate proper and don't mind improvising or homebrewing a bit, the appendix Baldur's Gate Gazetteer is an amazing resource with adventure hooks and encounter table for every region the city.  There's multiple campaigns of stuff to look through there.  After the Dead Three Dungeon is cleared, you likely have a Patriar's house disgraced out of power, maybe other family's and cultists too, making for a power vacuum, there's plenty of opportunity for intrigue or for adventurers to make their name as Baldur's Gate produces a new balance of power.  

The Descent into Avernus itself, I don't see it really all that flawed outside of less than noble heroic characters seeing the mission and going "nah"..  Yes, it's mostly a string of fetch quests interspersed with some pretty cool combats, and some odd role playing, but it may not be your thing, especially if the city of Balder's Gate is your passion, and you're comfortable running it, you could simply stay there.

EDIT: Duh, I forget Dungeon of the Dead Three was sort of the beginning not the climax to investigating the partiar family.  So to change my advice, do the Dungeon of the Dead Three, investigate the brother cult financier, then raid the matriarch of the patriarch family's house, including its dungeon.  At that point you've pretty much finished a starter campaign, if you think they'll want to "save Elturel," by all means play on.  Otherwise, you could task them as messengers to deliver the news to Candlekeep re: the fate of Elturel and then you pull stuff from Candlekeep Mysteries as the next phase of your campaign, or just have them go back to Baldur's Gate (or never leave) and have them get involved in the likely power vacuum and discord that'll likely occur when it's revealed a powerful family was once again in league with evil.  The party could have a direct role in working with one family or another or a Grand Duke, etc. creating a new balance of power.  Or they could sit out that fight and get up to anything you want to make up based on the broader info in the BG Gazetteer appendix.