in a spreadsheet column, so at the end of the year I can quickly sort and classify everything for taxes (and is a quick way to make a P/L statement if you are doing a re-fi at a bank)
FYI I also use a spreadsheet for all rental related bank deposits (which also is useful I’ve found out to show the tenant when they move out exactly what they paid in rent/security deposit)
As to the rest of the questions I consult a tax professional (BUT with spreadsheet showing what you income/expenses are it should make answering these other questions much much much easier)