You may have an older manual.  Page 15 of my manual (version 2.5 dated June 2012) is pretty clear:

"...apply a filet to the keel joint and the chine joints inside either side." 

"For best bond....add glass tape while filets are wet....and saturate with epoxy.....You can add tape later ... but the bond... won't be quite as strong."

I have not started my sailrig yet but the construction appears to be the same as the Chesapeake kayaks.  Watching the video series "Building a S&G Kayak" under the Tips for Boatbuilders tab of this site will be well worth your time.  #5 of the series covers filets. 

Clear coat the wood, and add the fillet in one step. Wet the glass tape separately, on a wet-out table, using a plastic spreader. Loosely fold the tape, carry it to the boat and gently lay/unfold it into the boat, lightly pressing/smoothing it into the fillet, and smoothing the sides. Some call this "kiwi-preg", sort of the poor man's version of pre-preg. You'll get a better resin ratio, and avoid lots of spills and drips this way, and your brush won't make mush out of the fillet. And, if you ever laminate thicker glass or carbon tape, you can be sure of your wet-out and be gentler to the fabric if you do it on a table, versus in place.

Wetting tape with a brush is very 80's!

Amen to everything nemochad says.

When I want to be really gentle to the fabric, I use a gloved finger instead of a plastic scraper.

Laszlo