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Should I be using the decontamination enzyme with my DNA extraction?

Only if you open a qPCR sample plate (or strip of tubes) post amplification/thermal cycling.

Quantitative PCR instruments measure the fluorescent signal from each well after each round of template amplification.  Once the thermal cycling program is finished,  there is no need to remove the seal from the plate, it can just be thrown away.

Contamination from previous qPCR products can be a concern if you remove the seal from a plate after thermal cycling is complete. In the event that any DNA products from previous reactions are unintentionally introduced to subsequent reactions, the enzyme used in our optional decontamination step will digest any DNA contaminants from previous qPCR tests.

The decontamination step can be very beneficial when performing end point PCR where you must remove plate seals to work with samples after cycling.  Methods such as DNA library preparation for DNA sequencing.  Read more about this process we've name 'DREAM PCR' in a peer reviewed paper we published: DREAMing of a patent-free human genome for clinical sequencing