It has a locked in low payment in an area of swiftly climbing rents.My question is should I use my HELOC to invest in a cash flowing 3 unit property, or start small and work my way up to that someday?

Most of the multifamily deals in Atlanta are at unusually low returns so I would be patient. 

The fee doesn't sound high at all and could actually be pretty low if that's the only fee.

I loathe this low barrier to entry/lack of buy-in that Zillow has created. 

It is surrounded by a cabinet shop on the left side, a couple commercial buildings in the back alley that are used primarily as storage for various businesses and a bar on the right side.

I have found low dollar works better than high dollar houses.  

HELOC is one of the best thing you can do with low apr. ttry wells fargo they give 60% ltv

I think the expense figures are too low - why only 3% for property management?

The VA loan is very low down payment (highest mortgage amount possible) and you have to owner occupy, right?

There is a Lowe's just a couple miles from the property.