System settings section contains settings that are not suitable for other sections and are used more by administrators than store owners.

Order ID - if you change this setting, your incoming orders will appear with higher numbers than the one set here.  
Task - delete guest older than minutes - you can define how long do you want to keep the guest's account in the store.
Task - days to cancel unpaid order - you can define after how many days store should automatically cancel unpaid orders.

The rest of the settings is intuitive so shouldn't be a problem to figure their meaning.