Good to see you on the forum.
Yes, starting the wrong configuration can be dangerous and we usually recommend locking down access to that using the Prognosis sercurity section.
To answer your question, both areas are perfectly fine to start a configuration but most people usually modify the running configurations in the Node Navigator window.
I have some tips for you for this area:
1. Check out the free Audit Log Solution available at: https://online.prognosis.com/forum/us-ask-the-experts/audit-log-extractor-track-prognosis-activity/
2. If you do make a mistake and start the configuration incorrectly, Prognosis does keep backups under the Document Navigator and "My DIsplays & Configuration\Auto-Saved Documents" (See screenshot at bottom for example)
I hope this helps.