CRA works fine with Marshmallow.
There are just a few things you've to look out if you want to use the syncing feature together with ComicRack for Windows.
First make sure that you've selected a writable folder for your comics on your device. Either keep the one ComicRack selected for you or use the Home-Button in the Main Comic Folder Preferences to select a folder on a different device storage (external SD-Card).
For Wifi-Sync you're all set now.
If you want to use syncing via USB, you've to make sure that your device is visible to Windows in MTP mode. Connect your phone, tap on the usb connection notification and make sure Transfer Files (MTP) is selected. If everything is fine, you should also be able to browse your phone's memory with Windows Explorer.
Optionally If you've put your comic folder on the secondary SD-Card you can also remove the card from the phone and put it into an SD-Card reader to sync it.
If there are any problems or questions, just head over to the User Forum.