MJ - my recently-completed Ches 17LT is still fresh in the mind, so my response is based on that: your query is not absolutely crystal-clear to me, but...
The fillets run along the inside of the hull from end to end: at the bottom of the hull in the cockpit area the fillet will be about 3/4" to 1" wide. Side panel fillets may end up a little narrower - it is not an exact science. Do not get carried away too much by 'nominated' width of filleting tools - I think you'll find that's just a guide and you will quickly work out what suits you and your level of expertise.
If your question relates simply to the extreme ends of the craft - yes, it's difficult if not impossible to get a tool in there to effect a nice smooth fillet, but a gloved finger will do a better job! If you leave the fillet to partly cure you will find that dipping the gloved finger into some warm water with a splash of washing-up liquid in it (acting as a kind-of lubricant) and simply working it along with some gentle pressure will allow you to make very smooth fillets indeed, almost looking like they came out of a machine.
I made it a little easier by chamfering the square cut-off ends of the sheer clamps to an angle (viewed from above) - much like the scarf joint in the sheer clamps - which gave me somewhat better access. A plastic throwaway teaspoon is a good filleting tool for some of the tighter angles, too.
Tape is applied to both the hull and (side) chine joints, over the fillets. Again, very tricky to get this neatly right into the ends, but nobody will ever see them (and so long as the strength is there it doesn't matter).
Finally, don't get carried away by the end-purs - if done to excess you will waste a lot of epoxy and add unwanted weight at the wrong ends of the craft. In my view and experience, soaking some 3" fibreglass tape in epoxy, rolling it into a cigar-like cylinder (very messy!), then ramming it into the ends is at least as good as an end-pour, easier (no need to tip the boat up), and probably lighter. About 12" will suffice for the bow, about 7" for the stern, and the result will certainly be more than strong enough in normal use. If you do this, keep returning to the craft after you've done the ramming so that you can scrape up any excess resin that will inevitably run out of the ends and down and along the bottom hull chine - again, a plastic spoon does an excellent job here.
I am following all the above well-learned lessons in my current Shearwater 17S&G build, so am personally satisfied with the results!
Enjoy the rest of the build.
Wordsmith