The IDE is definitely the way to go for downloading code.
However, if you still want to use germs, it is still there.
Add a legacy on-chip memory component (in SOPC Builder under legacy components).
This is the old memory component you are familiar with that has a contents tab
that lets you select germs. In the "More CPU" settings page of SOPC Builder,
make sure you point your reset address to the start of the germs memory and
set the debug device to one of your uarts.
Also, you might need to enable legacy SDK on the same page. I'm not sure about
this so try it without first.