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If you're talking about taxes, I file separate tax returns for my corporation (which has it's own EIN). The profit/loss from the corporation's K1 form goes on my 1040 (which is based on my SSN).
If you've been running as a sole proprietor under your SSN, there's a special form (I think it's called Schedule C) that's added on to your 1040 income tax return.
As for expenses, if the expense was for that business, you can deduct it. I do have a separate bank account under my corp. EIN to keep things organized. If you haven't already, hire a local CPA to handle your tax returns, so you can focus on growing your business. Hope this answers your questions.
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