Apologies for the delay - an unusually busy day cleaning up and fixing everything that was damaged in the storm that came through recently.
OK, what colors are you referring to? The UI theme colors? It should save to your config right away. The tool library is also saved to the config file. If there's a problem with your configuration not staying I'd like to figure out what's causing that.
Yes, so a lot of the functions are all applied to the layer permanently, except that you can undo them. What you can do is duplicate a layer to keep the original handy for making changes to. It was a bit of a judgement call as to whether or not different functions were more like modifiers or functions that were permanently applied to the contents of the layer. The main reason for choosing to make them permanent is that they're expensive to compute and constantly re-computing them would bring program responsiveness down. There are probably ways to optimize things a bit so that all of the raster editing functions are modifiers rather than actually changing the contents of a raster-layer but it's something I haven't put much thought into yet. I do like the idea of moving to that model though.
Another idea is to have PixelCNC at least remember the parameters used for the different functions, so that users can re-apply the same parameters multiple times. That would definitely be a pretty straightforward feature to implement on there.
Thanks for the feedback, I'll think about where to go from here for the next update after the beta release soon. Just wrapping up some website stuff for the launch and doing some final testing and then everything should be good to go!