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The return is due March 15 for the previous year. Your S-corp doesn't pay taxes, it files a form 1120S informational return. The 1120S produces a form k-1 that states your share of the companies income and other items. You report that k-1 on Schedule E of your Form 1040 in April. You have to file the 1120S every year whether you made money or not. Definitely find a professional, the 1120S is not easy to do.
You can deduct mileage for charitable purposes, currently .14 per mile (this rate can change annually), other travel expenses including meals, uniforms, and any other out of pocket expenses that are directly related to the non-profit. Keep in mind the non=profit has to be a charitable organization under IRS rules and these are itemized deductions, so you have to itemize to take advantage of them.
This isn't really a pro-con situation. If you're running a business you need a business account. If a bank finds out you're running a business through a personal account they'll close it. You also take a huge risk on veil piercing if you have an entity and you risk reclassification in an audit.
Documentation is going to vary depending on corporate structure and type of investment, but essentially it's going to be paperwork stating the date of the transfer, the amount, and what you received in return. Debt investment is different than equity.
Capital contributions (equity investment) and loans (debt investment) are not deductible until they are deemed uncollectible.
It depends on why you're going to IL. To be deductible the expense has to be ordinary and necessary to that trade or business. If there's a legitimate business reason then maybe, there are still limitations on how long you can live somewhere before it becomes your tax home. You're going to need to elevate this question to a tax attorney so you can go over it in detail.