You can do as as @ptrblck mentioned. Also you can just save their states_dict in a single file as-
torch.save({'encoder': encoder.state_dict(), 'cls': cls.state_dict()}, 'both_models_state_dict.pt')

And then load it later as-
both_models_state_dict = torch.load('both_models_state_dict.pt')
encoder.load_state_dict(both_models_state_dict['encoder'])
cls.load_state_dict(both_models_state_dict['cls'])