Emails

Does Hikashop keep track of communications with the customer. Like when I confirm their order I send them a tracking number. If they call me and want to know where there item is I can track it for them. OScomerce kept it all with the order information. also is there a way to make it easier to add a tracking number when you confirm an order?

HikaShop doesn't keep a copy of the emails you send to the user.
Normally, you create a custom order field so that you simply add the number in that field of the order before changing the status of the order to shipped and it is added to the order details for future reference and is is also added automatically to the order notification email.

Is there documentation or instructions on how to do this?

It's really easy so there is no need for documentation. Just go in the menu Display->Custom fields and create a new custom field of the table "order".