It can be handled a variety of different ways, but you’ll ultimately need to decide what makes the most sense for your organization. I often times will see GMI (Government Monitoring Information) collected on a separate sheet that is generated by you loan origination software.
To me, I would think that might be the easiest approach. You could also go with the alternative of the different application as you mentioned. You could create your own in-house document in Word to facilitate the collection of the information. However you choose to do it, just make sure you do it.