Your example uses it perfectly! You can use it in the same situations as “clear.”
“Are the instructions clear to you?”
“Crystal-clear” is an exaggeration, so it is used when you’re emphasizing clarity.
“I want to make sure the instructions are crystal-clear to you.”
This implies that these instructions are very important, so you have to understand it all very well.
We usually just say “clear” unless we really want to make sure the other person understands.
It’s used often by teachers in school. You can even use it as a verb sometimes—to “be” crystal-clear, meaning, to understand completely. But it is usually used like the examples above, as an adjective.
“Make sure you are all crystal-clear on what you need to work on today!”