Hi Mat,
This is something that comes through experience in watching the sky and clouds over many years though it will always be inexact. Knowing distances between you and hills or mountains can help you to judge how far away storm clouds are, and also how tall they might be.
You can also use the soundings to provide an estimate of where the tropopause is and subsequently what height anvils will be - though powerful storms will punch through this somewhat. The soundings can also be used to estimate other cloud heights, and what level the bases will be.
Eg: If there is an inversion at 4,500 metres, you might see cumulus congestus bubbling up and looking promising, but not getting past that height due to the warm layer preventing deeper convection.
MB