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Thanks for reaching out!
Since you are not using an Arduino sketch to program the APDS-9960, I suggest you to use Avago's documentation (http://www.avagotech.com/products/optical-sensors/integrated-ambient-light-and-proximity-sensors/apds-9960) instead of SparkFun’s.
In the sensor's datasheet you'll notice that there is a section specific for the color and ambient light sense operation. I believe you should start by reading the details found in there (page 13 of the datasheet http://docs.avagotech.com/docs/AV02-4191EN). Nevertheless, I would suggest you to read all the instructions that the datasheet include after page 8, it is very detailed and should be of help for your project.
I hope you find this information helpful.