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What determines whether bi or di is used as prefixes of two?
Is there anything that determines if scientific terms use bi or di or is it just sheer luck. example are the di in number for compounds that have to pairs of an element like carbon dioxide. bi in lipid bi-layer that make up cell membranes

" They are different from each other in the origin and usage. The main difference between Bis and Di is that Bis  is used to denote the presence of two identical but separate complex  groups in one molecule whereas Di is used to denote two of the same  chemical group in one molecule."

Source: http://pediaa.com/difference-between-bis-and-di/