Saving to the cloud happens whever you save your project .pad file. It creates a backup of the .pad file in the cloud. This has nothing to do with deployment to apps though, for that you need to 'publish to app' to compile the project ready for transfer to the app. If deploying via the cloud, you need to publish the compiled project to the cloud with this button:
Screen Shot 2016-11-13 at 20.17.23.png
This is so that you can work on a project .pad file, saving backups to the cloud as normal, without the intermittent changes automatically going live to the customer's app - if they had 'Automatic Cloud Sync' turned on in their settings.
'Synchronize PC files with cloud' does pretty much the same job as saving a project which is already cloud based - it sends all project files to the cloud. if the project is not already cloud based, it lets you add it to the cloud. The only difference between a save, is that it overwrites all image files with the ones on your PC - sometimes needed if you alter an image file manually, it wouldn't usually be sent to the cloud again.
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