It is important that you understand how Splunk permissions work within app contexts, because this affects where Splunk stores .conf and other files, reports, dashboards, and alerts, as well as how it controlls who can see and use or alter these reports/dashboards/alerts. A few sample scenarios using the example of creating a new report would probably be helpful for you to underastand these concepts.
First of all, if you are going to create a new report, you should consider who you would like to be able to find and use it. If it is generic in nature and meant to be visible to the Splunk user population at large, you should perhaps create it within the Search & Reporting app, since that's where most people usually ...