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.
The entirely unsatisfying answer is, “As much or as little as I have to.”
I haven’t run a 5e adventure, but I imagine that would require a LOT. Part of this can’t be helped, because in any long campaign, you’re going to have to be more flexible to account for the unexpected and accommodate your players. The other part of it is that D&D’s design philosophy seems to be “eh, fuck it, if it’s broken, people will just blame the DM and say it’s their responsibility to fix it.” A part of this is the entire CR system (in a game that focuses so heavily on balanced combat encounters, no less), so I’m not surprised that tinkering with combat counters is so necessary and so frustrating.