You can use hold to overlay multiple plots on one set of axes. The following code demonstrates the concept using stem3 to plot the datasets.
% Random inputs
A = randn(20,3);
B = randn(20,3);
figure;
% Create a 3-D stem plot for dataset A
stem3( A(:,1) , A(:,2) , A(:,3) ,'blue')
hold on; % Activate hold
% Create a 3-D stem plot for dataset B
stem3( B(:,1) , B(:,2) , B(:,3) ,'red')
hold off %turn off hold
legend('A','B')
