Yeah, You are correct.
The Engine harness is the main one. It is the larger of the two and connects the DME to the engine and fuse box. It can be completely removed without cutting any wires. If you look to the left of your fuse box, you will see three round connectors, those are the connectors that connect this wire harness to your car.
The other wire harness I like to call the front wire harness. It connects the minor things like your headlights, horns, fog lights, ect. This one will have to be cut near the fuse box if you want to remove it.
If you are interested in replacing the engine harness, their are a few styles, ect. You will need to know the year of your car and the options you have.
Is their a reason you want to replace yours?
As a side note, I am currently selling both/either wire harness form a 98 manual 318ti with traction control. If you are interested, let me know.
http://www.ebay.com/itm/221633463918...84.m1555.l2649 I can do better on price if you PM me. =]