Nupic will give you one anomaly score from a multi-field data stream yes. I think downloading nupic and looking at the one hot gym example is a good place to start. In that instance nupic is being fed 2 fields, one for energy consumption and one for time. There is a really good video on youtube that walks you through this example:
You can theoretically add as many fields as you want, simply by adding them to the model parameters file. It is recommended to try and limit the number of fields as much as possible though, certainly no more than 5 per model. If you have many fields you can make numerous nupic models with several fields each, or one model per field.
Finally there is a process within nupic called ‘swarming’, where nupic looks for which of the possible fields are most helpful to predicting the ‘predicted’ field that you specify. If you want to share what your data looks like (first few lines to get a sense) that can help to advise you. Best of luck