Holes are made of bank, through which the sap runs into clay cups or shells placed ready to receive it.  句中的bank似应为trunk（树干）。

关系代词在定语从句中作介词宾语，介词短语作状语，在正式语体，介词+关系代词位于定语从句之首，引导定语从句。非正式语体可以将介词留在原处，由which引导从句。但本句中runs还有into介词短语作状语，如果将through留在原处，形成runs through into clay cups...则容易让人误以为through是个副词。故还是将through和关系代词which一起前置为好。

holes, through which the sap runs. 正是语体

holes, which the sap runs through. 非正式语体