I was a bit confused by a homwork problem that I was working on. The problem is that I found the flux of a charge and I know the demsions of the Gaussian surface it is encolsed in. It doesnt seem right intuitively to be able to find the location of the charge from this information....but mathmatically im thinking I can solve for r.
$$\Phi=\oint _\mathcal{S} \mathbf{E}\cdot d\mathbf{a} = \frac{q_{enc}}{\epsilon _0}$$
and since electric field is the flux over the area i can find it by
$$E=\Phi/A$$
so shouldnt I be able to find the position fo the charge from
$$\Phi/A=q/4\pi r^2 \epsilon_0$$
this is really confusing, do I have the theory wrong?

Yes, you have two different definitions for flux:

$$\Phi = E A$$

and

$$\Phi=\oint \vec{E}\cdot \vec{da}$$

Notice how the second definition is a generalization of the first one. The first equation only applies to flat surfaces which are perpendicular to the field, the second definition works in general.

Also, the r that you pulled out of Gauss' law is the radius of a spherical Gaussian surface (an hence the place you are looking at the field) , not "the distance to the charge".

THANK YOU, that makes alot more sense now!