I coming from a flat saddle (front to back) to a Fizik antares (flat with raised rear)

when setting height on the antares should I use the raised or flat portion for reference for saddle height? or maybe somewhere in the middle?

If you position the saddle with the front horizontal and the back tilting up, then try measuring to the horizontal part. That is probably where you are sitting most of the time.

Best way to measure seat height is by riding...

^Same here. I rough it in by measuring, but it's impossible to correctly measure sitting height on a curved surface. After measuring, I ride the bike on the flat, unclip one pedal, put my heel on it and continue to pedal. My heel should barely touch the pedal at BDC with a locked knee. But even that isn't accurate enough really, so the next thing is to see if I feel the correct amount of power in my leg at the bottom of the pedal stroke. I know what it's supposed to feel like, or at least what I like it to feel like, so that's my final check, maybe a mm or two refinement. The first couple of rides I put my multi-tool in my jersey pocket and probably stop a couple of times for adjustment.

This is pretty much how I rough it in, but I prefer to do it stationary while holding on to something. It really depends whether your a flat foot or toe down rider. As you get it dialed in, it may take a few longer rides to make the final few mm adjustments.

Measure to where your butt goes.

I like this approach! For me the way my foot feels at BDC is related to how easy it is to spin fast, so I can only set that up on a turbo trainer or on the road.

Me to. I make a dot with a white out pen at the sit bone location which I take to be the widest section of the saddle and use that position to measure height and also distance to bars.

I always measure inline with seat tube and seat post and top of saddle no matter where it lands on saddle . Then ride for final adjustment.

Are you guys actually using a tape measure? I know the height my saddle should be by standing next to the bike and putting my hand on the saddle. It should be right ...... there!

When purchasing my first good ten speed I did that and the mechanic at the store said how do you know that's the right height without sitting on it. I told him all my bike saddless are right ..... there!

Long hours in the saddle.

I actually use a tape measure. And a laser x/y level. The problem with the method you've described is that it doesnt take into acount any differences that there might be in bottom bracket height.