You can use external tracking scripts for extensive tracking capabilities such as entire site visitor tracking scripts, order tracking scripts that track conversions/visits. Below are some guidelines on where you can place your scripts:
Where to put General Tracking Scripts:
You can place general tracking scripts in the footer under Themes > [Active Theme] > Page Footer.
Where to put Order Specific Tracking scripts:
You can place order specific tracking scripts under Store > Store Settings - scroll to the area 'Integration Settings' and place the script with the script tags in this area:
The script will be added to the bottom of the ViewOrder page.
The script can reference order based merge codes to populate order information.
This script will only be inserted and run one time per order and will be right when the order is initially placed.
The script will not be shown when a credit card is declined.
The primary purpose of this area is for use with external scripts that you may need to run only one time per successful order. An example being the customer survey run through Shopzilla which needs to be run only once per order and not everytime a customer views their order. Though additional information for the customer could be included here, it may not be an ideal location and the location cannot be changed.
Where to place Google Analytics Conversion Tracking Scripts: