I use the "configurable usb loader" and it works fine through a forwarder.
Forwarders just point to a certain location on the sd card or usb drive, there is no magic to it, just make sure the folder is there and contains the application files and your done. The forwarders are the way to go as many of the applications can now auto-update, if you are using an embedded channel then your software will not update. Not to mention it also uses up precious wii memory.
As far as fat or wbfs, it is really up to you. I preferred wbfs in the beginning, but that was just a compatibility thing, now the support for fat is robust and pretty solid so wbfs is not needed. I use fat now as it allows me to store other things on the drive that I may need.