I load the stem & wood WPA via straw pack, then tamp with the tool.
I scoop the flower out of my stash for the 18/14mm glass injector bowls with the bowls, tamping with the tool.
I don't use the funnel for anything.
Cleaning the wood portion of the WPA is simple as the wood is just a removable sleeve. Just lather with wood wax / polishing balm / wood cleaning product of your choice, let soak for about an hour, then wipe dry. The glass portion can soak in iso separately. I use Ed's as a cleaning / finishing solution, but any should work. I don't use the wood WPA often, though, I much prefer the injector bowls, so it doesn't get a lot of grime for me to truly test. I do however use Ed's wood WPA for my tm2, and that has gone through multiple cleaning cycles and still is perfect.