I can't tell you about the Fort William beats in the lower river, but I have been fishing the Blackwater for 25 odd years now. I own one of the bungalows next to the Lodge.
I usually use a floating line with an 9ft leader and tippet of 2ft. You won't usually need a sink tip unless the water is high or you want to fish the slower deeper pools.
As to flies, I use GP's most of the time in average water, in orange, black, purple or red. Pink Polar bear shrimps also work
Ian and Glenda will advise as to the best flies though, so don't worry.
If you are ONLY fly fishing make sure you tell Ian & Glenda that as A LOT of people spin the river too.
If it is high then you could try the Cork Bandon which is more of a spate river (quick up and quick to fall) or dry fly trout fishing on the upper Suir with Andrew Ryan of Clonanav FF, who apparently also have access to private salmon beats of the Suir.
Another alternative is the new stillwater fishery on the road to Dungarven - cappagh Lakes.
I would fly to Shannon and have Ian hire a car for you - you need a 4x4, as some beats are a very long way from the road.
Oh, and get some Euro coins at the Airport or in England - you'll need them for the highway toll outside the airport.
The Lodge no longer offers dinner, so you'll need to eat out - River Action in the village is nice but a bit pricey. The village pubs do tasty hearty Irish fair at a good price, plus a fine pint of Murphys stout.
or, on the way back from fishing you can grab a Thai or Chinese in Fermoy, which also has a small fly shop up a side street.
Enjoy it - I always am there in the last week of September.