What RAID function? The single bay My Cloud is not a multi bay unit.
What specific problems are you having with the My Cloud? What software are you using to backup to the My Cloud?
As to your main question, yes you can use alternate software, many do, for local network backup or local network syncing TO a single bay My Cloud unit. Remote backing up or syncing via third party non WD software/apps is a different story. Officially for remote access one uses the WD software/apps or the MyCloud.com user web portal, or one can use the very insecure FTP option of the My Cloud. Unofficially there are several methods for remote access (SFTP, SSH, WebDAV) that are not supported by WD. One can use the forum search feature (magnifying glass icon upper right) to find various other discussions on using SFTP, SSH, WebDAV, etc.
Here are some free programs for backing up data from a PC to the My Cloud on the local network. Free File Sync can be used in mirroring mode for backup or in sync mode to perform file syncing.
EaseUS Todo Backup Free: http://www.easeus.com/
Macrium Reflect Free: http://www.macrium.com/reflectfree.aspx
Paragon Backup and Recovery 14 Free: http://www.paragon-software.com/home/br-free/download.html
Free File Sync: http://www.freefilesync.org/
There are any number of other paid and free backup programs that can be used provided those software/apps provide the ability to backup to a local network device like an NAS.
Quite a few of us, including myself, do not use any WD software/apps at all for local network access.
