If you slap an 'EXPLAIN QUERY PLAN' before your query, it will show you high-level information about how it will perform your query. This should show you the indices it is planning on using.
For more information, see: http://www.sqlite.org/lang_explain.html
If you are to the point of 'locking down' your database, and you need to ensure SQLite is using a specific index, there is a construct for this. Be aware that unlike other database engines, it is not a hint but a requirement. Your query will be forced to use this index, and if it cannot, it will fail.
For more information, see: http://www.sqlite.org/lang_indexedby.html
Hope this helps some.