Most of my clients that invest in Jax are mainly doing fix and flips.

Maybe you are crushing it so much it is now your main revenue driver.  

There are many factors to consider when investing in any market, but the main things I work with my clients on are price point, level of rehab, exit strategy, and risk tolerance. 

These are the main reasons so many investors have turned to these types of commercial mortgages.

Been around a lot of that mainly on smaller SFR deals. 

I think starting off that would be my main focus multi family in the future.

As @Nick Harrington stated the main drawback as I see it is that you are buying at retail or very close to it.

I'm mainly focusing on Old Town, but would be open to Del Ray or Potomac Yards.  

For example, should I have one checking account that manages all expenses, such as down payments for properties and serving as the main source for rehab budgets?

The main argument against it is that you could use that money to continue investing and make a better return, but if you aren't going to use it for investing anyway and it helps you sleep at night go for it.