Wouldn't any existing Images folder of my own, be over written the second I push the Save button in Juicebox?
Yes. If you save your gallery to a folder which already contains a custom 'images' folder, then the contents of your custom 'images' folder will be deleted.
I'd recommend that you save your gallery to a new empty folder of its own and then make the required changes before adding the gallery files to your web project.
... just wondering if there is a way to edit the config file before pushing the save button.
No, unfortunately not. There is no way to change the name of the 'images' folder or to use custom paths for the imageURL entries from within JuiceboxBuilder.
If you save the gallery to a folder of its own, then it would be very easy to just keep the gallery in its folder (without needing to make any modifications to the contents) and embed the gallery using the baseUrl method that I mentioned above.
... is there any way to make the Thumbnail size a percentage instead of fixed pixels (or make it responsive somehow to the viewport).
No. The dimensions of the thumbnails can be defined only in absolute pixel values (and not percentages). The gallery itself will remain responsive (changing its layout to suit the available space) and this may result in fewer or more thumbnails being displayed per thumbnail page, but the dimensions of the thumbnails will always remain fixed (at the specified thumbWidth and thumbHeight values), no matter what device is being used to view the gallery. (The size of the main image and the number of thumbnails displayed can dynamically change depending on the size and shape of the browser viewport but the thumbnail size remains constant.)
I realise that this might not be the answer you were looking for but I hope that it at least helps to clarify things.
I dont mind there being less columns in mobile, but 1 doesnt work so well.
Perhaps the best course of action would be to compromise and set your thumbWidth to a value which gives you at least 2 columns of thumbnails on your small screen devices (and accept that this will also result in smaller thumbnails in desktop browsers, too).
Hopefully you'll find a balance that works.