Both Arche and Logos are abstract concepts which were believed by their respective creators on how the universe was held together.

It sounds okay, once you add some pauses with commas. Try this…………………

***Both Arche and Logos are abstract concepts, of which their respective creators believed, were the substance, or idea, that held the universe together.

Here’s my suggestion:

The creators of both Arche and Logos believed that they (Arche and Logos) are abstract concepts and the substance or idea that held the universe together.

Both Arche and Logos are abstract concepts which their respective creators believed were the substance or idea that held the universe together.

The creators of both Arche and Logos believed that these concepts were the substances or ideas that held the universe together.

or

concepts, which

(no of, and if you say which, you need a comma)

grammatically, creators is correct, but factually it is incorrect

Make substance and idea plural, because they are modifying both, or reword your sentence to avoid that awkwardness.

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