@Zak,
You can use the USE INDEX feature in your query and pick the one you want.
source: https://developer.couchbase.com/documentation/server/4.1/n1ql/n1ql-language-reference/hints.html
From there you can use the visual query tool(PLAN) to see for a give query how efficient an index is for you.
VS
CONSOLIDATING INDEXES
You might want to consolidate indexes too
VS
