I've been using whole leaf hops from Freshops just thrown in the wort. After cooling, I use an autosiphon without any filter on the end to get as much wort into my ale pail as possible. I have to clean it out a few times as it gets clogged with the whole leaves. I tried putting a hopsack over the end of the autosiphon but it clogs almost immediately and find it works better without. When I get most of the wort out of the kettle, I put a 5 gallon sanitized paint strainer over the ale pail primary and pour in the rest of the wort.
This method is working well for me. I may begin avoiding the autosiphon all together and just pour, but this way the kettle isn't as heavy and it is easier to keep an eye on the trub without as much liquid.
Whirlpooling never worked at all for me with whole leaf hops.
Dry hopping in the secondary with loose leaf hops is no problem. I put a sanitized small hopsack over the end of my autosiphon, and just siphon to the bottling bucket. The hopsack filters any seeds or debris from the whole hops, and I don't have any problems with clogging the siphon.
Once you get a system down, I find it easy to work with Whole Leaf hops.