I second the comment about setting aside enough money for taxes because you are taxed at a different rate than those who receive a W2 vs. 1099
1. Familiarize yourself with IRS rules on deduction of expenses, specifically rent and home office deduction eligibility. (The answer to your question..NO, a cup of coffee/meal at a cafe cannot be counted as rent, but may be deductible if it fits the guidelines for Meal deductions, remember to keep your receipt and what it was for specifically.
2. Be organized. Keep meticulous records and save your receipts. Use a ledger, spreadsheet whatever works for you. Personally I track my expenses in an Excel spreadsheet and update it on a weekly basis. My gig isn't big enough to justify a Quickbooks purchase yet, so Excel works fine for me.
3. There are some great books to get at the library regarding home-based businesses and being an independent contractor that addresses many issues regarding expenses, what kinds of records to keep, etc.
4. Maximize your tax deductions by familiarizing yourself of what can and cannot be deducted. Don't stretch the truth when filing your taxes, the IRS does not mess around.
5. Yes, I would keep a separate account for your side business.
As for how it would work using your bike as a transportation expense...you might want to ask a tax expert if maintenance, etc is deductible. My guess is no...but a tax professional might know better.
Good luck!