Upon further inspection, I noticed that I do not need to break them into cases, and can just refer to the part under the square root within the if statement like so:
AT = sqrt(s.*(s-a).*(s-b).*(s-c))
if s.*(s-a).*(s-b).*(s-c) < 0
AT = sqrt(s.*(-1.*((s-a).*(s-b).*(s-c))))
end
%The new issue is that sometimes I get back a triangle with an area of 0.
%hmm.. Ok - the 0 case is when a = 20, b = 24, and c = 4. Matlab does this
%math: sqrt(24.*(4).*(0).*(16)) = 0