Watermarks visible during DNA fingerprinting?
The "watermarks" that you're referring to sound exactly like DNA fingerprints: stretches of DNA that are unique to an individual. These unique stretches occur naturally in all individuals, but specific artificial sequences could theoretically be inserted via techniques such as CRISPR.

Once inserted, these artificial sequences could be searched for specifically through PCR, if the sequence is known, or through traditional enzymatic restriction methods, such as described in the first link. 

It's worth mentioning that in order to be easily detected, your watermarks would most likely have to be inserted into the germ line of these genetically modified humans. Otherwise, you'd only be able to get the watermark sequences into a small region of tissue. Once in the germ line, the body's own DNA replication mechanism takes over copying those sequences throughout the organism. 

Good luck writing!