There's no reason to "feel dumb" about this: when you described the kind of course you had, it explained something about the approach taken, which I'm afraid is not very effective at giving insight into physical situations (but which is, unfortunately, pretty common nowadays).
You can think about the displacement as a line connecting the starting to the ending position. The direction and length of that line would be the same regardless of what altitude you decided to call "zero" and start measuring positions from, so it is independent of the choice for an origin.
To answer the other part of the question, we started by calling upward "positive", as indicated by your choice of equation
<br />
y(t)=vt-\frac{1}{2}gt^2+a.
If we instead chose downward to be positive, but kept the origin at a distance a below the starting point, then the starting point would be above the origin, which is now in the negative direction from "zero". By the same token, the upward initial velocity is now also negative, and the direction of gravitational acceleration is now positive. So the position equation would become
<br />
y(t)=-vt+\frac{1}{2}gt^2-a ,
which of course is just the negative of the one you wrote earlier. The displacement between the initial position y(0) and the later position y(T) would now be
<br />
y(T) - y(0) = [ -vT + \frac{1}{2}gT^2 - a ] - (-a) = -vT + \frac{1}{2}gT^2<br /> .
This is the negative of the result you had before for the displacement, which is just what you would expect from reversing the direction of the y-axis. So the displacement is also independent of the direction you choose to call positive (that is to say, the displacement is still upward by the amount indicated, but upward is "negative" here).
This is something to keep in mind in working with many physical quantities: if their values or the physical situation does not depend on the point of view, then the result should be the same regardless of the choice of origin, of axes, etc. (This is the basis of the concept of "physical relativity", which can also extend to choice of the velocity or acceleration of the observer.)