-Should I have separate accounts for each property?
No. One business bank account is enough and much more simple. As others suggested, do not mingle personal and business transactions. Some states require you to have a separate bank account for tenants security deposit, if not, one is fine.
-How or where do people scan in physical receipts?
Some accounting software (like QBO) let you attach documents in the transaction. There are also apps available but I prefer doing it directly in the accounting software or something that integrates with it.
-What is the best way to calculate and keep track of all expenses and cash flow both monthly and yearly for each property?
A good accountant/bookkeeper and/or a good software.
-What is the best system to be best prepared come tax season as far as having everything organized for my CPA and having the documentation I need in case of an audit?
I highly recommend using Quickbooks Online, especially if you are planning to use a remote bookkeeper or CPA. As far as documentation, I recommend keeping electronic copies of at least all closing statements, loan docs/statements, and bank & credit card statements. Google Drive or Dropbox are some of the free cloud storage and can easily be shared with your accountant if needed whenever and whereever. If you will use an accounting firm, some have a client portal.
-Where are state specific lease agreements that I can access for land lording?
BP has those forms if you're a PRO member.
Goodluck!