ActiveSync is the best method to use, though either will work. With ActiveSync your SkyDemon unit stays on, and a little message flashes onscreen when sync is complete and the software loads the new data in real time.We've been doing some work on making the install/sync process more robust ready for the next version. If you encounter an error during install such as the one you mentioned, it probably means SkyDemon is already running and therefore the files can't be overwritten. After a failed installation attempt like this a sync may not work properly (something we've addressed).
Install should only be used to initially install SkyDemon Mobile on a device. After that, sync takes care of most things including upgrading the version of SkyDemon on the device.