Now that GPU crunching has finished ( :( ), what has to be done in settings?

I changed my device profiles. Do I need to do anything with that app config file?

Just noticed my machine was doing nothing, so I've already changed which projects I'm on ( and those device profiles).

No need to do anything with app_config.
Just make sure to set Yes for "Allow research to run on my CPU?"

Do you still want work for your GPUs?

I've found that PrimeGrid 1.39 PPS (Sieve) (atiPPSsieve) is reliable in maintaining WUs for a GPU. http://www.primegrid.com/
Some projects like SETI do not keep a flow of work coming for the GPU.
Also, for my ATI7770 GPUs, I can set the app_config file for 0.03C + 0.5ATI or 0.03C + 1.0ATI depending on the system.
That way the GPU WUs don't interfere with the 8 CPU WUs. At least it works that way with my Intel i7 systems.
You kind of get your cake and can eat it too.
I think this also works for NVIDIA GPUs, but I haven't tried it so I can't promise anything.

If your app_config file was set to reserve some CPU cores to feed your GPU then you might need to get rid of it (save it somewhere for next time ;) ) otherwise just re-enable the other projects and you should be good to go.