First off, you need to remember that, at 12 weeks, he is still very much
a baby. Another thing to remember is that you have to teach a dog that "sit" doesn't just mean "plant your butt on the floor when we are in the kitchen", it means "plant your butt on the floor no matter where we are", which takes time and patience.
Clickers are great for baby puppies, but you have to do it right. The first thing you need to do is build value for (aka "load") the clicker. That is as simple as taking a dozen or so treats (can even be kibble) and doing rapid fire click/treat until all the treats are gone. Don't ask for any behaviors or anything, just make that click "pay". Do this a dozen times or so a day, and pretty soon, just seeing that clicker makes him happy.
Training actual behaviors can be done through shaping (waiting until he does something you want, then click/treat) or luring (him following a treat that you are guiding him into position with).
This would be a good resource. Fenzi Dog Sports Academy - FE110: Raising a Performance Puppy
Don't let the "performance" in the title scare you, as it's a good foundation for all puppies. It's a retired class, meaning that while you will have all the instructor's lectures and videos, there aren't any live forums.