Do you mean Character Atk and Elemental Atk? For some reason the Elemental word is omitted in Eidolons.
I'd say that it matters more the higher you go. However, keep in mind if you play with elemental advantage and an offensive Relic weapon, you already have 75% Elemental. So if you have ~120% Assault, 75% Elemental and your own Eidolon is Amaru, then you're at ~120% Character and 120% Elemental. Thus, if you pick a 45% Character Huanglong or 45% Elemental Amaru will give you the same amount of damage output.