So I flipped the yak over and inspected the bottom, and noticed that over time Ive gotten a couple of good scratches along the hull, and a few rough spots. Its not bad enough that it might cause a leak or something, but I was just wondering if this was something that I needed to sand down and/or epoxy to fill in the scratches. Thanks.

i am wondering the same thing mine yak has some bad scratches too

Red,
If your 'yak is of the rotomolded variety try using an old clothes iron. Yeah, I know; it sounds goofy but, it works. It's much safer than using a blow torch to melt the plastic and will not remove the plastic like sandpaper will. It just melts the loose plastic back into the affected areas. Uh, don't use the "steam setting"; the steam generated by the iron prevents the plastic from melting back into the gouge or scratch... The iron will only melt the plastic in a very narrow "corridor" on the hull and should be effective except where the shape of the hull prevents the iron from getting into the tighter radius of the hull. Worked very well on the bow area and the flat areas of the hull on my T120. I don't think that epoxies will adhere properly to the polystyrene...
Just my two cents...

Unless they are leaking consider them battle scars and leave it alone. I've seen people cause more harm then good trying to repair a kayak that really didn't need repairing.