What can you use your knowledge for?
What for can you use your knowledge?
--- Are both OK?
I much prefer the first.
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"what" is actually the object of the preposition "for", so your second sentence should, in my opinion, read as:
For what can you use your knowledge?
"What for?" could mean "why" in the right context.
E.g.:
- I'm going to sell my house.
- What for?