An effective and easy way to build a canoe or kayak anchoring system is to use a mushroom anchor, which can be stowed in a heavy-duty 2-gallon plastic bucket with holes drilled in the bottom. The bucket keeps the anchor and rope off the deck and out of the way, and the bucket also can be used as a drift sock.
Mushroom-style anchors are less likely to get hung up on rocks or brush than folding anchors. This is important for safety when anchoring in deep water. Another good alternative for anchors are old window sash weights.
After dropping the anchor to hold the boat in place, tie the rope to a thwart using a half-hitch knot. The remainder of the rope stays in the bucket and out of the way. You can also toss the bucket overboard and tie of the rope off to use the bucket as a drift sock.
This system works well with the Sweet Anchor Board, which attaches to the bow or the stern and holds the anchor rope at the end of the canoe. This keeps the boat from swinging in the wind at anchor and also keeps the boat tracking straight when drift fishing.
The anchor board can be cut out of 3/4″ marine plywood.