There's a tooltip when you mouse over these settings which describes what they mean.
Gantry height is the vertical clearance between the build plate and your x-y gantry (on the Ultimaker, these are the 6mm shafts which hold the head).
If you print two objects - one after another - then the first object must be shorter in height than the gantry height. Otherwise, the gantry would crash into the first part while printing the second part.
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IRobertI 516
If I'm not mistaken all measurements are taken from the nozzle tip. So, for the first one, measure the size of your head from the nozzle tip towards the direction in X to where your machine homes.
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