-create or have a web project with two or more java source roots, say src (default) and src2 (custom)
-create some @WebService class in the src2 source root
-create a Bottom-up web service from the class created in previous step

=> generated classes are in src (default) java source root but I'd expect them in src2 (custom) source root since the class I used is there or I should have an option to choose where to put generated classes

for Top-down ws there's no way to say where to put generated stuff

If I choose to use Axis, I'm given an option to specify target source folder, if I use JBossWS I'm not given any option