How to identify when to change Indexes
Since you are on S1 you can use two features from Azure:


Query Store
Index Advisor.


With Query Store you'll be able to identify the bottlenecks, the most heavily usage queries and the plans they use. This will allow you to prioritize what queries to optimize, and which existing indexes are important. 

Index Advisor is more than missing indexes, see this video. It has some ML modeling that allows it to pick the most impactful index recommendation, eliminate duplicates, and it does A/B testing to measure the difference.

In general tables that already have 5-6 indexes and you find yourself adding more are good candidates for clustered columnstore indexes (supported on Azure and on premise post 2014). Segment elimination can do miracles for you.