Typically your insurer will seek to recover your deductible.
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I would go through your own insurance as it will be much faster. Your insurance company will surrogate against the motorcyclist and include your deductible in their claim.
I would file the claim with your insurance company. Let them go after the motorcyclist's insurance company. Your insurance company has a duty to recover the deductible if they can. Also you may be able to just get a check for $3,300 and fix only what you want to or can fix for that money. Unless your policy has language which requires you to fix the car, there is nothing in the law that requires you to repair the car with the insurance proceeds.