It's exactly that, aggregating two or more physical ports to create one logical one. It increases the bandwith of the link. It also provides redundancy without worrying about looping. If one of the physical ports goes down you will still have connectivity.
There is only one STP instance for the logical port, not multiple STP instances for each port in the aggregate.
As far as configuring in Juniper, I will let someone else address that as I am still learning Juniper myself.