I am not sure I understand your question but perhaps this will help.
If you want to divide your data set into a design set and your own validation set you can do that before training.
During training with TRAIN many of the training functions will divide up the design data into training (for optimizing the error gradient), validation (for measuring generalization in order to stop training at optimal generalization), and test sets (for an independent test).
As long as you have withheld your own validation set from the training function, it can be used as an additional independent test using SIM of the network beyond those that were selected for that role during training. You can provide all the validation vectors at once, as columns of an input matrix, or loop through each sample calling SIM with one column vector at a time. The results will be the same either way.
For PATTERNNET the outputs represent class probabilities, but as independent estimates which may not add to 1. If you need them to add to 1 you can either normalize the output by dividing by their sum, or change the output layer's transfer function to SOFTMAX before training:
net.layers{2}.transferFcn = 'softmax';
SOFTMAX ensures output vectors sum to 1.
