Argh, I feel your pain! Resolution is my bane. My laptop can only do so much so I basically push the highest resolution possible. I'm no good at these atlas style maps - having never really tried - but I can say that I have had the same problem...It's hit or miss with your first few attempts and you just end up starting from scratch once you nail down the basics. I'm a bit of a technophobe so learning to use image editing software is like pulling teeth, for me. Basically my way around this problem is to start with the highest resolution you can, make invisible the layers that slow down the software so your brush doesn't jitter around, make plenty of backups and resist the urge to flatten layers for the sake of performance. You can always export to a lower resolution but you can never go to a higher one without some form of distortion.