Jesse, I was born in Champaign, IL, so I am sure I can help your thinking )))
First of all, Auto Move should not be disabled and should always apply to the default capture folder. I use SC sometimes to move around, and am bewildered when I find Auto Move is no longer working.
At the very least, I think that whenever SC is started it should start at the default capture folder, and not where it was the last time it was used. This will help reduce the confusion and mess that is caused when new screenshots or scans go into some folder where I've focused SC, as by the time SC is restarted (in my case at reboot) that location is no longer important.
It has been an annoyance to me when I've edited files in other folders with SC and then later took a screenshot to find it was put in that other folder. I've had to mentally remember, countless times, that if I move to another folder I MUST REMEMBER to move back to the default folder for subsequent use. This has actually caused me to be hesitant to use many of the navigation features of your program because just looking around changes where the captures go! If it is any help, in my opinion, new screenshots don't need to go wherever the program is focused, as I don't use the program to create screenshots in other folders than the default folder. I use it save or manipulate images in other folders, but not to create new ones in other folders. So the default folder is where I want new screenshots or scans to go, and from there I may navigate elsewhere only to manipulate or save images.
I vote for "moving around to subfolders would not have any effect on where new captures are saved." But as for the separate issue "what should happen if you are in a different folder and a new capture is made" I would vote for a new capture leaving the current folder and going to the new capture in the default location. You can spruce that up for people who want to put screenshots in all sorts of different places with a configuration option to disable the default screenshot directory which is always used for new captures. In conjunction with that Auto Move should always apply to one directory only (specified on that configuration page).
I hope this helps.