2 Layer power routing with mixed signals
I haven't looked at your files. ...In general, for a two layer board I would put the bottom layer to be a ground plane and keep the power delivery traces short and wide on the top layer. 
There will no doubt be places that the signals will need to cross, and it's fine to take them on to layer 2 but be careful not to make any copper Islands and not to break any continuous ground underneath the power delivery. 

It is almost certain that you need to keep the copper away from the bluetooth module because it will mess with the antennae. Are there any impedance controlled nets in your design? If so this might be more difficult on a 2 layer board



Okay I have had a look at the png images on your github page and its not clear what you are asking. I can see 2 traces under the module: pin 38 bt_led and pin 28 select. Both of these can easily be moved onto L2 and I would suggest stitching vias on either side. 

Your biggest problem is the chunk of signals on the right hand side passing directly underneath U2 and L4. These will pick up huge amounts of noise from the switcher. They must be routed somewhere else or move the psu to be above a ground plane

As for your specific question, the avdd is already separated from the rest because you have them joined at the smps output. D1 is the only thing that also uses this trace, but I don't imagine it will be particularly fast. So not a problem as it is. You should definitely decouple the other supply to the module at pin 14, and possibly add some lower value ceramics alongside c1. 10n perhaps