Help with Idle Speed Adjustment

OK, I'm a little confused. I have a 1999 SeaRay 180 Bowrider with a 3.0 Mercruiser and Alpha One Drive. I believe I have a couple of things going on. The boat cranks and runs excellent when cold, but when it warms up it has a tendency to "deisel" when I shut it off, then afterwards it's really hard to start. I went to a local lake last Sunday to let the kids do a little waterskiing. After a couple hours of running I slowed to a stop and put the control in "Neutral" and the RPM's didn't fall...it stayed around 1800 RPM. I lifted the engine cover and it appears the throttle linkage is not returning to the stop. I read the section in the book that came with the boat on setting idle speed and it either gives conflicting info, or I'm an Idiot. At first it says Idle speed must be set with the boat in the water, in gear and control in idle position...the it says( in the next paragraph ) Idle speed must be set with the engine in "Base Timing Mode" and control in "Neutral" Which is the better, or Correct way to accomplish this? Thanks...and sorry for being long-winded!!

Re: Help with Idle Speed Adjustment

Everything that I have seen says to set the idle speed and mixture in gear with the engine warmed up.. There are preliminary settings you can do out of the water.
I don't know what Base Timing Mode is.. so I can't say much about that.