Please refer to the following image.
Based on the formula, graphically speaking, to obtain the area of the region bounded between the two curves $y=f(x)$ and $y=g(x)$, I am supposed to subtract the area of the shaded region in graph $2$ from the area of the shaded region in graph $1$ so that I can get the area between the two curves.
I can understand why I should subtract that small portion (bounded by the graph $y=g(x), x=b$, and the $x$-axis), but I cannot understand subtracting the portion (which lies below the x-axis) bounded by $y=g(x)$ and $x=a$ and $x=c$, where c is the $x$-coordinate of the point where the graph $y=g(x)$ cuts the $x$-axis. I cannot understand why this must be subtracted because this portion was never part of the shaded region of $y=f(x)$ anyway! It seems as though I am subtracting something unnecessarily! Can somebody explain this, visually if possible?
Note: In both graphs $1$ and $2$, I have included the other graph in dotted lines.

The way the problem is set up you shouldn't subtract the area above $g(x)$ from the area under $f(x)$ geometrically speaking because areas are not defined to be negative(which why we often use absolute values in such situations). In fact to get the area of the shaded region between the two should be added. Remember that the area given by an integral with respect to $x$ is the area between the bounded region and the $x$-axis.
And, if you must perform/understand the subtraction geometrically then one way to do it would be to add some constant $c$ to both function such that $g'(x) = 0$ (to make sure the minima touches the $x-axis$) for some $x \in [a,b]$ Basically if you add some constant you raise the graphs of the functions up so the your $g(x)$ has it's lowest point touching the $x$-axis giving you set up you need and then subtract the integral value of $g(x)+c$ from the integral value of $f(x)+c$. For example, below $c = 4$ and it has been added to both functions so you as you can probably eye ball the area between them is the same, although in the case of the functions with the added constant you will be subtracting positive areas. This will be subtraction of two positive areas in the conventional sense of geometry.
Hope that helps.