I understand that this may be hard to know, but I can see some ways people could know. Perhaps some words that come from pre-IE languages in Europe could be found in different languages. Perhaps there are similar place names from Pre-IE, for example next to rivers or another feature which would give the names similar words.
hi! There's lots of room for more information here, and I'm not sure that any of these will address your title questions directly, but you may be able to infer some information from these earlier threads on pre-PIE languages of so-called "Old Europe"
How much Pre-Indo-European vocabulary did Indo-European languages absorb? Which Indo-European language has the highest amount of non-Indo-European words? - no info here, but a link to an interesting resource