Don't know if there is a built in command to alternate, but it's straight forward with a plugin. Note that if you do not have 2 groups, nothing will happen.
import sublime_plugin
class PaneSwitch(sublime_plugin.WindowCommand):
def run(self):
window = self.window
if window.num_groups() != 2:
return
active_group = window.active_group()
if active_group == 0:
window.focus_group(1)
else:
window.focus_group(0)
Create a plugin with the above content. The command you will bind to is pane_switch
.