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 customize commercial adventures regularly and pretty extensively. I find buying and running the adventure in some digital format to be very helpful. If I buy a Foundry adventure, editing everything is a built in feature. If I buy a PDF, I copy text over from the PDF into my own digital notes and edit them. This way, I end up with a fully integrated adventure with whatever I want to pull from the commercial text integrated right along with whatever changes I want to make.