I've often had to do similar repairs on pieces of furniture I've built.  I use 5 minute epoxy and mix in some wood dust and fill the gouge with the mix.  You want to over-fill it so it can be sanded back flush once the epoxy sets up.  You can use the wood flour that came with your kit, or make some sanding dust from whatever wood you're trying to match.  It usually winds up a little darker than the surrounding wood, which often works very well and can look like part of the knot. 

Some wood workers "stabilize" the knots with epoxy before working the wood, especially if they want to keep the knots in the work. This keeps the knot form wroking lose at a later date.

You might try putting the edge of the plane's blade against the edge of the knot and tapping it lightly with a mallet across the knot. Press down hard on the plane while you tap it to keep it from skipping. Keep the depth of the blade very shallow and the blade sharp.

Assuming you're going to cover the knot with fiberglass, you can fill small gaps or pits with resin and wood flour or a mixture of fine sanding dust and resin mixed to the consistency of peanut butter. Apply and then after the filler passes the fingernail test, sand it smooth and glass it. Don't use glue and wood dust.

You might also drill the knot out and plug it with a piece of matching wood or a dowel, but a dowel will have end grain exposed and be dark. If you have a friend who's a wood turner, they can turn a piece of wood for you the size of your hole with the long grain of the wood on the surface. If the wood matches, you can line up the grain and it will be hard to notice.

You can also chip out the surface of knot with a small chisel, carve, sand and fit a piece of wood that matches the surrounding wood. Glue it in place the best you can, sand it down and move on. Unless a knot is huge, when you glass it it won't make any difference as far as strength goes.

As soon as I finished the last post, I realize there's a better, simple answer.

First, don't worry about the gouges now, you may find that in the fairing and finish sanding, you may sand them down enough that you don't even need to patch them.

At the start of the fiberglass process, wet the knot with resin and see how dark it gets. Then mix some dark wood dust and resin and see how well it matches. Adjust the darkness with lighter or darker dust and patch the gouges with the dust/resin mixture.

Thank you all so much for the feedback. Happy holidays to all