Traditionally I have run mostly homebrew adventures. I've used encounters taken from commercial adventures every once in a while. The Dragonlance campaign I'm running is the first I've really tried to run a module straight.
My players aren't always going along with that idea but that's ok. I've also added some content because I wanted a special event for the character with divine powers. I plan to do the same for the knight. Due to this I created Dulsi's Dragonlance Addendum on DMs Guild.
For Spelljammer I found the process less satisfying. I had to tweak many individual encounters to match what I wanted. So running it requires looking at the adventure and looking my notes for things to override.
I am returning to playing RPGs for the first time in well over a decade this year. I ran a few modules in my first life as a rpgista, starting with the adventure that came with the red dragon black box of Basic D&D. Later, I ran the introductory adventure that came with DragonLance SAGA and Sunless Citadel, for D&D3. But I ran them without modifications.
Now, many years since I last did any playing or gming, I am running "The Lost Mines of Phandelver", but I am changing quite a bit of it. Mostly because of the dislike we have for what was done to Forgotten Realms after D&D4. So, I pushed the adventure back to 1368 DR, what required some changes. Some of the ruins weren't ruins in 1368 DR, so I had to change places or repopulate other places using my old AD&D2 and D&D3 books for Forgotten Realms. It was more work than just running the module straight out of the box and even making my own homebrew adventure on my own homebrew setting.
Despite the extra work, that I welcomed after so many years without RPG, I am finding it very gratifying making that module my own, and I am already preparing to continue the campaign organically, without a hard cut. Hopefully, nobody will notice when I change from the published module to my own stuff in the campaign.