I wanna put subs in my hybrid but there is no way to go through the car to the main battery is it safe to hook everything up to the hybrid battery in the trunk?

The car has 2 battery systems. Make sure you go to the battery that goes to the engine. Don't use some crazy high power amp, go with 300 hundred watts or so to be safe.
We installed a system in a car like that had no problems at all.

I would seriously doubt it. The hybrid battery is most likely a different voltage.

that hybrid electrical wasnt designed to support anything other than the electric components in the hybrid part of the car. you will have to drill a hold in the fire wall or find a hole already. make sure you run the wire through a rubber grommet to keep it from chaffing.