I have the following system, specified by the set of coefficients:
b = [1 2 3];
a = [1 .5 .25];
In the Z-Domain, such function will have the following transfer function:
H(Z) = Y(Z)/X(Z)
So the frequency response will be just the unit circle, where:
H(e^jw) = Y(e^jw)/X(e^jw)
Do I just substitute in the e^jw for 'Z' in my transfer function to obtain the frequency response of the system mathematically, on paper? Seems a bit ridiculous from my (a student's) point of view.

Have you tried
freqz()? It returns the frequency response vector,h, and the corresponding angular frequency vector,w, for the digital filter with numerator and denominator polynomial coefficients stored inbanda, respectively.In your case, simply follow the help: