uses a specific naming convention for indexes it creates. Indexes created with use the i<TABLENAME>_<key value> convention. If you are using indexes created outside of the application, you need to make sure the index names match the naming convention.
Performance is affected by the number of indexes you may have. If you use tables with multiple indexes, keep in mind that when a record is written or updated, locks are put onto all of the indexes, and they are all basically rewritten during the course of the write/update. This is a costly process. There may be multiple columns per index, and multiple indexes per table. Each rewrite implies a certain amount of wait time. Tables with a large number of indexes can be slow on writes/updates and possibly other operations in the database query optimizer become confused.
For more information about indexes and performance issues, see Performance and Troubleshooting.