Join Operation using index defined?
TokuDB is a storage engine in MariaDB, as is XtraDB/Aria/MyISAM. Queries are planned by the upper layers of MariaDB (and MySQL) calling into the storage engine to help it make decisions about optimization.

What you need to do is


create your tables and load your data
create the indexes you think will help optimize your query workload
run your queries with EXPLAIN


The EXPLAIN output will help you see that good decisions are made based on your indexes.