If I have a 5V top layer/plane, and a GND bottom layer/plane, how does FZ know to not connect the 2 together when you add a THT part - I’m assuming all THT parts are plated holes in the PCB -.
Yes holes for THT pins will plated. At least assuming the part has been defined with both copper0 and copper1 layers for the pin.
To avoid connecting the layer/plane, you “fill” the ground and power on the appropriate side in pcb view after parts have been placed, and routing has been done. Fritzing will avoid the existing copper and keepout areas (non plated holes, board edges) when it fills the layer.
Actually, avoid the copper that part of a different net than what is being filled, so the the ground and power connections WILL attach to the filled area.
I thought there would be a problem, so it’s SMD only.
I was doing a tutorial and playing with ground fill - I’m not a FZ superuser - and I got it to work, but then I remembered plated holes. You set a seed on one net, set top layer, and ground fill that. Then deselect that seed and seed the other net, select bottom, and ground fill that. I now have a 5V top copper plane and a GND bottom plane. I wonder if you can put a copper blocker right across the bottom of the PCB so it’s split in two, and use the seed, fill, swap seed, fill, etc, so that you get 3 separate planes, ie, 2 GND planes and a PWR plane. 
Doh, you can do top and bottom GND planes with THT because the opposite GND fill makes a keepout.
GND fill.fzz (15.7 KB)
You can’t do a split GND fill/plane, ie, 2, on one side. When you put a copper blocker on half the PCB and seed and GND fill one half, that works. But when you move the copper blocker over the GND filled side to protect it when you GND fill the other, it deletes the 1st GND fill. I was hoping the copper blocker would preserve the GND fill like it does the traces.
Should work the same with SMD and a double sided board.
Messy, but you could use the blocker, ground fill one half, export, move the blocker and fill the other half, then in post processing merge the fill area from the saved export.
I should’ve known you would’ve know.
I’ve only done a few circuits, and only one had GND fill, so it was interesting playing around with it, plus there was an old post asking for split GND’s. At least we know how to do it now.
At least know a way that in theory should work. I’ve never actually done it. How messy that merge will be is unknown.