Whirlpool solves some problems with running traps in general.
The problem is, you want to rez your ice before a trap so a runner doesn't get spooked and realize you want him to access. However, if your ice stops the runner, he won't access and he'll realize it's probably a trap if you don't score it the next turn.
On the other hand, if the ice is rezzed, an intelligent runner can tell if it's a trap or agenda with a decent success rate. If the ice is breakable, he'll assume it's a trap, and if not, he'll assume it's an agenda. This makes sense: why would you put a trap in a server he can't get into, and why would you put your agenda in a server he can get through? For this reason, it's often advisable you randomize your decision of whether to trap or agenda, but it will still backfire from time to time.
This is where Whirlpool comes in. It allows you to make a new server and put a trap behind and rez Whirlpool forcing them into it, or you can simply not rez Whirlpool if there's an agenda there and rez the other ice. Additionally, Whirlpool works well behind a Chum as a guaranteed 3 net damage in addition to forcing the runner into the trap. For this reason, I always advise running Whirlpool instead of Data Mine in the vast majority of Jinteki decks.
So to answer your question on Whirlpool's use more succinctly, after you have a rezzed server the runner's run on a couple times, make a new, unrezzed one. The runner often thinks you're attempting a more secure server. Place a Whirlpool on the outermost layer, putting the server at 3 or 4 total ice. Now play and double-advance a trap or agenda and Rez accordingly. The nice thing about porous ice (such as Katana or Chum) is that you can Rez them after activating Whirlpool and the runner can't simply neglect to break, ending the run.