What is the difference between もと ( 本) and もと (元)
In my textbook they are both presented as meaning "origin".

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Oh, I see. I will focus on learning the Kanji combinations then. Thank you very much!

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There are very slight difference between them.
Even in Japan, very few people know the difference.

Originally,
「本」is used to represent something which is related to basis or essence.
¨「元」 is used to represent something which is related to origin, cause, root, or money resource.
But every phrase with these kanji does not always follow this rule.

I recommend you to just learn some words which uses these kanji.

例
資本（shihon)　capital, fund