I haven't fished Skye, but have fished for trout (mostly) and salmon (a little) in many parts of Scotland. This is all fly fishing, but I assume you knew that. The usual procedure (for me) is to consult a guide book (Rivers & Lochs of Scotland: The Angler's Complete Guide. by Bruce Sandison; the latest edition I have was published in 2009), which tells you what's available on a day ticket and where to buy the day ticket at. I just checked Amazon and they have a Kindle version for $6.79. I'd buy that, then Google the places that looked interesting to see if the arrangements for obtaining day tickets have changed since the guidebook was written.. I generally tried to choose waters that I could buy a day ticket at a shop, rather than calling up a club member. You could also just stop in a tackle shop and see what day tickets they have available.
For what it's worth, I prefer fishing rivers and hill lochs over large lochs. Generally, the brown trout aren't very big, but fun to catch.
Salmon fishing is not necessarily horrendously expensive, but generally the low cost means low chance of catching a salmon.
I hope this helps.
