I'm almost to the point where I will need fillers and laminating glues for my boat. I basically need, as far as I can tell:
1. Something for filling the gaps between strips
2. Something for fairing out the dips and hollows that shouldn't be there.
3. Something to act as a glue between the keel/stem laminates.
4. Something to glue the keel/stem to the boat.
 There are so many choices of fillers available. It's kind of confusing. Silica or milled glass or cotton fibers? Glass bubbles or phenolic microspheres? Wood flour?Â
I used wood flour/silica for most of what you describe with the exception of fairing the deck and hull. I use microballoons to make a bondo type epoxy mix. Wood flour and silica are hard so if you use them shape it as well as you can using a spoon, bottle or something else to get close to the shape you want in the grove where your planks and stem meet. Sanding epoxy with wood flour and silica is harder then microballoons by at least a factor of 10 but the finished joint will also be very hard which to me is a good thing. The micro balloons sand easier and make a nice easy to spread bondo when mixed in epoxy. I also used graphite to coat areas that I thought would gain from being smoother and slicker like the insides of my dagger and mast boxes as well as inside the rudder assembly. I didn't always add silica. I don't like the stuff. Powdery, super fine dust that sticks to almost everything because of static and if you ever get it in your eye, from wiping sweat or dust in the sir you will wish you had never opened the container it came in. It does seem to make the mix smoother.
I filled the screw holes, heads and small nicks in the wood with the left over wood flour mix from joints. It works but make sure you scrape off any extra before it hardens and be careful sanding as the fill is harder then the wood around it so you can end up with donut shaped areas around those small fills if you sand to robustly. I filled the small holes and areas, scraped off any extra, let it harden and then finished off the area with the microballoon bondo mix later.
You don't have to make large batches when adding fillers. I have made batches of 2 drops resin, 1 drop hardener and a pinch of wood flour. I did that small a batch to see if it was feasable and to get myself into the idea that I didn't have to make so much epoxy each time. I have dozens of little epoxy wood flour pucks that formed from left over mix that settled in the bottom of the plastic cups I used to mix in. There are times, like when wetting glass cloth or coating the deck, that you need to make fairly large mixes and in some cases more then one batch but I found that buying a cheap set of mixing spoons and mixing smaller batches saved me a lot of epoxy. Many of my batches were tablespoon sized. Typically 2 tbls resin, 1 tbles hardener and 3-4 tbls of wood flour.
I used plastic spoons, plastic cups and paper kids cereal bowls for most of my mixing. They are cheap, don't take much room in the trash or can be burnt in a wood stove or barrel after they harden. I tried the pumps that came with the epoxy but they were messy and not accurate enough to use without some measurement so I just pored into the measurers from the cans. For the large batches I used the plastic cups for measuring. Just be aware that the hardener may disolve the pastic cup if left to long so don't set up a bunch of cups with hardener and resin to speed up second and third batch mixes if you use them.
There are three categories of thickened mixtures I use: heavy structural, light structural and cosmetic.
A heavy structural mix will always have 'glass fabric on top and typically would be milled fibers and/or wood flour and/or cotton flock (West 403) and/or West 404 (powdered calcium) and/or West 405 (mostly cotton flock and silica, with some wood flour) and of course fumed silica (Cabosil).
A light structural mix will have the same filler options, but may not have the fabric over it.
A cosmetic mixture will have micro balloons, spheres, talc (baby powder), Q-cells, etc., plus silica to control viscosity. Sometimes a cosmetic mix will have a light fabric over it.
Silica's major role is to control viscosity, though it also makes it really hard. The percentages of fillers to each other depends on the tasks and no two are the same. For example I use a high percentage of milled fibers when bonding to 'glass. If bonding wood to a 'glassed surface I'll use some wood flour, but still a lot more milled fibers. If bonding just a 'glassed surface to same, no wood flour, just milled fibers. If bonding wood to wood, I'll use a little milled fiber, but lots of wood flour or cotton flock (403). For a fairing compound the cosmetic mix is the call, so no wood flour or milled fibers, just one of the "bulking agents" like micro balloons or Q-cells and a touch of silica to control viscosity.
This is the "Cliff's Notes" version. Both West System (westsystem.com) and System Three (systemthree.com) have user's guides to download free and they cover the material choices more completely.
I used the blended filler from duckworks for pretty much all the filling and filleting. It has a brown color when mixed so you can't use it on anything bright. I painted everything except for the tiller so it was perfect for me.
The pre-blended filler from DuckWorks is micro balloons and silica, which is a fairing compound. Balloons have no real strength and are a "bulking agent" intended to make the mixture smooth and easy to sand. This is fine for cosmetic work and for fillets that are taped over. This filler isn't very good for structural work, bonding or used as a glue.
The fillers and 'glass products from DuckWorks come from E-Boat here in Vero Beach and commonly known as Bateau.com on line. You can save some money dealing with them directly. While on the phone with them or their site's forum, you can find out about their products and the appropriate uses. If you do call (suggested) talk to Joel, as he builds and works with these products each day, knowing them well.