George, it really depends on what your goals and expectations are for the system. If you want to send some sound back to the rider, but don't want to break the bank, making use of the stock amplifier will do the job.
I'm not familiar enough with the stock system on your boat to know exactly how everything is setup, but from your posts, I highly doubt the stock sub is run off of the 4 channel amplifier. With only one sub in the boat, that would require it to be a Dual Voice Coil (DVC), and the Clarion marine sub used in Mastercraft's does not fit the bill.
Also, be careful about the power output you're quoting. It looks like the APX480M has a continuous power rating of 80W x 4 @ 4Ohms. Using the front two channels to power the Deafcon Reference IIIs means each speaker will get approx. 115W @ 2 Ohms. That's under powering the speakers quite a bit, and I don't think you'll fully appreciate what they're capable of.
I would recommend picking up a small 2 channel amp that can put out 200-250W into 2 channels @ 2 Ohms. Use that amp for the Deafcon's and run the rest of the system how it is (or run the sub off the rear channels of your Clarion amp, and run the four boat speakers off the front channels). The TRU T-2.100 would be an excellent choice in this application: http://www.wakeside.com/page/W/PROD/tru_technology_amplifier/tru_technology_t_2_100
You'll be MUCH happier with the sound quality, and you'll really get the most out of your system. Adding a second amp is not a huge undertaking, but if your time is valuable, take it to your local car audio shop and have them do the job for you.