Welcome to the Apple community.
If you are referring to Mamut/MYOB accounting software, unless it's different to mine (granted, I'm using accountedge plus) it includes a provision to back up to iDisk rather than iCloud. iDisk has long since gone and is nothing to do with iCloud.
Perhaps you could check exactly where it's supposed to back up to.
The following is from this Apple document: iCloud: Backup and restore overview.
What is backed up
You get unlimited free storage for:
- Purchased music, movies, TV shows, apps, and books
- Notes: Backup of purchased music is not available in all countries. Backups of purchased movies and TV shows are U.S. only. Previous purchases may not be restored if they are no longer in the iTunes Store, App Store, or iBookstore.
- Some previously purchased movies may not be available in iTunes in the Cloud. These movies will indicate that they are not available in iTunes in the Cloud on their product details page in the iTunes Store. Previous purchases may be unavailable if they have been refunded or are no longer available in the iTunes Store, App Store, or iBookstore.
You get 5 GB of free iCloud storage for:
- Photos and videos in the Camera Roll
- Device settings (for example: Phone Favorites, Wallpaper, and Mail, Contacts, Calendar accounts)
- App data
- Home screen and app organization
- Messages (iMessage, SMS, and MMS)
- Visual Voicemails
Only apps that are designed to sync to iCloud, i.e. Keynote, Numbers, Pages, etc. can sync thru iCloud.
You can put anything in to iCloud either manually or with a script/automator, so it wouldn't be out of the question for a software developer to do so. Here's a screenshot showing that I can get MYOB to back up to iCloud.
In the OP's case though, I think they may be confusing MYOB's built in ability to back up to Mobile Me with iCloud. However I know there's a new version of my software out for the start of the new tax year for use starting next week, so I can't say for definate it doesn't use iCloud.
Yes, think of DropBox, it works the same way. The online store and the Mobile Documents are connected so that the content of one is reflected on the other (after a delay for internet transfer)
Nothing new, nothing particularly useful (for me) I dislike having to use a folder other than the one I would like to use for file storage. There are some 3rd part apps that do the same thing out there as well.
I dislike having to use specific folders, I much prefer just to save the file as I always do, so I use SugarSync, which allows me to keep the folder structure that makes sense to me while sharing any folder or file, or entire folder tree as and when I choose.
I use 3 computers and an iPad, every file in my user/documents folder is available on any of the 4 machines, in the same location as the original. That's simple enough for me,