How do you use Past perfect and past simple correctly?

Past perfect -- had + past participle -- is often used with past simple to show that one thing happened in the past before another thing in the past. eg

The train had left -- past perfect

I arrived at the station -- past simple

The train had left when I arrived at the station.

Another example:

The prisoner escaped -- past simple

He had been in prison for two days. -- past perfect

The prisoner escaped after he had been in prison for two days.

On its own past simple is used to write about something that happened in the past and is now finished. eg I went to the cinema yesterday.

Past perfect can also be used in the 'if clause' of a conditional statement eg

If you had eaten your lunch you wouldn't be hungry now