When I click yes, the first file is overwritten by the second.
In order to avoid the possibility of galleries being overwritten, I recommend that you save each gallery to a different folder. This keeps all galleries separate from each other and helps to keep things organized.
If you like, you can create a new empty folder for each gallery (maybe on your desktop) before building your gallery with JuiceboxBuilder-Pro. Then, on the 'Publish' tab, navigate towards this folder (via the 'Browse...' button) before saving your gallery inside it.
If you have all your galleries saved into individual folders, you can then upload the complete gallery folders (not just the contents) to your web server and embed the galleries into your web pages using the baseUrl method documented here.
Second issue, when I open Juicebox Pro and go to "open gallery" nothing happens.
When you click 'Open Gallery' you then need to navigate towards the gallery folder that you want to open. Highlight the gallery folder (do not go inside it and select a file) and click 'Select Folder'.
If you do not get a pop up 'Select Gallery Folder...' window when you click 'Open Gallery', then close JuiceboxBuilder-Pro and delete the following folder manually before re-opening the application and trying again. This should hopefully help.
Mac: /Users/your_username/Library/Application Support/Adobe/AIR/ELS/JuiceboxBuilder-Pro
Windows: C:\Users\your_username\AppData\Roaming\Adobe\AIR\ELS\JuiceboxBuilder-Pro