Tuning a Proform/Holley carb, what parts and tools?

I am watching the Holley tuning video, and it was saying if you don't remove some fuel from the bowls first you will bottom out the floats. Does this not apply to this carb because you can lower floats with the engine running?

Not sure what "bottom out the floats" means, but if you lower the level slightly, you shouldn't need to remove fuel. I guess if your fuel level is waaay to high and you lower it to the bottom, it may put strain on the float's arm since the float would then be submerged in fuel. Shouldn't be an issue with minor adjustments though.

I have heard conflicting info on where the fuel should be in the window. In the middle or at the very bottom, which is it on a Proform/Quickfuel?

I'll defer to the 'experts,' but I've always run the level even (or close to even) with the bottom of the window. Keep in mind that float level adjustments may change AFR slightly.