Sorry for coming to the kayak trolling party late. I spend a lot of time trolling the finger lakes in kayak. Started out years ago with couple of paddle-only yaks, and eventually upgraded to a Hobie peddle drive so here's my $.02
One of the biggest challenges you'll have is getting the right depth depending on what species you're targeting and what time of year it is; rather than try to cover all that, I'd suggest searching the site - based on people's reports, you can get a pretty good idea of what depth you'll need to be at and what lures / colors are producing action.
I can pretty much cover any part of the water column from the surface down to 160-180 ft depending on how I'm rigged for the day.
Starting from the surface working down, here's my set-ups:
For flat lining, I run either mono or braid, and add split shots for added weight.
I have rods with 4 & 5 colors of 15 Lb. Sufix Performance Lead Core with 20-30 Ft of a Fluro top shot. With this set-up I get approximately 7 ft of depth per color, and can use a deeper diving lure to get additional depth.
Torpedo divers attached with OR-16 snap weight clips to braid (with Fluro leader). Full disclosure, I've donated a few of them to the lake bottom, because they are easy to lose when trying to disconnect.
Down rigger - run either a 2 or 4 lb. ball with 150 Lb. braid line. Can get down to 180 ft with the 4 lb., but do get enough blow back that I can't see the ball on sonar. I can run 2 rods off the down rigger, with 1 release attached to the ball and 2nd on the rigger cable attached with a OR-16 snap weight clip.
Have a rod with 10 colors of lead and a shorter 7 ft leader.
In the earlier days, ran a 3-way swivel with different weights and lures to get down there.
Have tried a variety of dipsy divers / slide divers / jet divers, but never really got consistency with the depth they run, so don't use them anymore.
A few quick pointers:
Lead core in a kayak takes patience - it's slow deploying until the first color or so are out and it gets enough drag to pull itself off the rod - keeping the rod pointed straight back also helps.
Running multiple lines helps to vary your presentation and (hopefully) get more fish. It can be a challenge to keep from getting tangled up when hooked up. I try to keep the yak moving forward instead of stopping to land the fish.
I also only use trolling reels for trolling- When I got into kayaking, I was running 40-year-old Penn Peerless 9's that I used as a kid with my father & grandfather. I've since upgraded to mostly line counters, but still use a couple of the Penn’s from time to time. Spinning reels are used for jigging or casting.
I run a lot of 40+ year old Spoons from my grandfather. Sutton, Pine Valley & Miller are some of the brands I still have. Have a bunch of different stick baits – Berkley / Rapala / Kabooms / all shapes sizes and colors. Can't say that any one specific lure is a 100% catch-all, so I switch things up if not getting hits.
One of the advantages with the yak is that if you find a spot holding fish or bait pods with fish under them, it's pretty easy to get turned around and keep running through them .
Like others said – vertical jigging is a blast in a yak.
Lots of you tube videos on kayak fishing. Lots of us have posted in this site about kayak fishing - use the search function to find the posts.
PM if you have other questions.