updating foo.ui after changing ui_foo.h

I am using the Qt plugin for Eclipse. I have a foo.ui file and a ui_foo.h file. I modified something in ui_foo.h. How do I get that modification to show in the foo.ui file? Also, is there a way to automatically generate a foo.ui file from a ui_foo.h file?

You don't. You shouldn't modify autogenerated files.

Is there a way to add custom widgets to the Widget Box then? or a way to add custom widgets to the .ui file? If so, where is the documentation for it?

See Qt Designer Manual:

• Using Custom Widgets with Qt Designer
• Creating Custom Widgets for Qt Designer