I have been primarily using it to finish the heads of my baitfish patterns and really like the way it brings out the color of the materials/ brings the color to the surface. That's why I would like to find it in larger containers than the 2-part syringe.
Anyway, I just squirt a small amount into a dixie cup & mix with a coffee stirrer. I start off by putting a small drop where each of the eyes will go, get those where I want and then using small dollops again, work the epoxy around the edges of the eyes, filling the void between them and then down the nose to the eye of the hook, slowlly pulling it along.
Based upon the quality of the sample flies of yours I've seen, I find it hard to believe that there are really any noticeable bubbles in your finished products.
Maybe it's the epoxy. Lately I've been using Superglue's 5 min. epoxy and really like it - it has a crystal clear finish.
Dave P also suggests 20 minute epoxy, Domenic recommends 1 minute.
I've also read about Red Devil having an acrlyic caulk that dries clear and is much easier to use - haven't found it yet.
PS - I'm always ready to play hooky!