It wouldn't matter as long the difference is between the two function and then integrated within bounds.
Basically, when you integrating a single function with bounds. You are just taking the area between function and x-axis as (y)−(0), y=0 is the x-axis.
But now, you are finding area with respect to another function below it. So, it doesn't matter whether graph of second function is below or above x-axis.
If you want to verify this consider the value of
$C_1:y=x^2$
$C_2:y=2x^2-1$
at $x=0$,
$C_1(0):y_0=0$
$C_2(0):y_0=-1$
And the difference? Well that's $C_1(0)-C_2(0)=1$ .
So, it wouldn't matter whether one of the graph goes below x-axis! As long as given that, you are integrating in form of $\int_a^b y.dx$ where bounds a,b corresponds to point on x-axis!
Here's the graph.
https://www.desmos.com/calculator/f6fffrpz0w
And the area you require, can be easily calculated by:
$$\large\int_{-1}^{1}x^2-(2x^2-1).dx$$
Without caring for whether $C_2:y=2x^2-1$ goes below x-axis. However be careful when only a single function is given not involving any difference between two function which demands you explicitly finding TOTAL AREA.