Thanks JBS for the kudos. And, yes, there is no way to stay out of this one. And, there are way too many issues above to not comment or try to help.
As you can tell, Jon, has a very good and well thought out backup plan, and you also never heard him talk about turning off SQL Server. You also never heard him talk about something taking an hour. Here is some info point by point that I hope helps:
1. You should NEVER have to turn off SQL Server to do your backups. If you do, then your backup software is just not good enough. And, you do NOT have to turn them off to run AC. If you did, Jon (the other Jon) would have built that in to the program.
2. Separate point but pertaining to above. There will always be a P2P vs Client/Server debate on here. But, I think the difference between AC's efficiency is negligible compared with what you are forced to do when you are running a server. Again, Jon, has overcome that as he has been a long time user and is very computer savvy. You can't use $49.00 backup software and expect it to back up SQL properly.
3. A little about SQL Server. SQL Server consists of SYSTEM databases: Master, Model, MSDB, Temp, etc. Programs which use SQL as a database install/attach to SQL and form an instance. So, in your services on your PC, you will see SQL Server (AMAZINGCHRTS). That is one instance. You may have two or ten depending on how many applications are using it. A server OS will have several intrinsic programs using it as well. The AC instance contains three USER databases: Amazing Charts, Meds, and Codes. These are user databases and aren't running when no one is using them. AC's backup backs up these and a few other folders needed to restore the instance. The SQL Server engine which works with AC and other instances does run constantly. For SQL backups and all of its instances to be consistent data on the drive, some type of program must do this. SQL Server has its own program to back up its data, but this is really not necessary. If you use a program that doesn't get all worked up about .mdf and .ldf in the SYSTEM databases, you will likely get a decent back up of your AC folder with the user datbases.
4. What to use? Well, first, if you are using non-server OS, you will not be able to get backup software that will work as well. CAVEAT: That is not to say you can't. I can't look at all of them. But, a quick look at Acronis (one of the industry standards), shows client backup software to be anyway from $45.00 to $95.00 while server backup software is $950.00. The latter is all you need to back up SQL as it is is an image and backs up as a snapshot. It is actually extremely good software. If you want the standalone SQL Server backup so you can back up AC and SQL Server every minute (takes < 1 second to make these backups), it will only set you back about $700.00. I am not recommending these, but just giving a perspective.
5. As far as .enc file. Basically, as Jon said, you HAVE to back up II separately. If you are getting away with it now, that's great. Do it at night, and one hour is no big deal. My server backups take three hours.
6. Again, as I always say, general to specific. Forget everything and just start with an entire backup of your computer. Every night. The whole thing. And, back up to multiple hard drives. Now, here is something that is not coming up in these discussions. If you have any version of WIN7, you already have an extremely good back up program which utilizes VSS. It will make complete backups as well as set you up with one System State Full Metal Backup. It is simplete to set up, will find any of your backup destinations and uses Microsoft's block technology to save on space. It will also show you how much space you have left on your drives.
7. VSS. Volume Shadow Service produces Volume Shadow Copies. Many applications and backup programs are compatible with VSS. When you backup program starts, VSS comes on and goes to various programs like Oracle and SQL, etc. and basically commands it to stop and "commit" its data to the hard drive. And, it is serious. The apps will listen to it, and using VSS writers, then write all of their data into frozen data which is then backed by your program. The nice thing about VSS is it creates retore points AND (bonus) previous versions. So you may have 30 previous versions of AC's folder and not even know it. It does this with many folders. I believe XP Pro used it but not to the extent that WIN7 does.
8. Strategies to backups. There are as many strategies to backing up data as there are users on the board. Personally, I got tired of the Grandfather/Father/Son backup strategy along time ago. Yes, I overdo it, but I like mystem. Ten external eSATA drives with multiple full backups and weekly backups to two RAID5 NASs in the basement. I do three small backups to one of the drives manually. Yes, I take home a backup weekly, but, frankly, I forget most of the time. Which is why I use JungleDisk online, which is the best online backup.
9. Deduplication vs Incremental vs Differential. Incremental takes all you changed files and makes a backup. If you have 20 of them, then all 20 have to work plus your original full backup for it to work. A differential takes longer but is safer as on any given day you can just use that day's differential and combine it with the full backup. But, these two are archaic and use up way too much bandwidth compared with deduplication, which as its name implies, doesn't duplicate anything. So, if you back up, say, email. If you sent out the same email to 20 staff, an incremental backup would look at that and say everything was different and back it all up. A deduplication system would say, yes, it is all different, but why back up all twenty. We'll just do one. And, even more fascinating, if you back something up that already exists, it will just set up a point to that other file or sub file. Say, you have the first paragraph of the Gettysburg address backed up. If you then back up the entire version, it will leave out the first paragraph and just point to the other file. So, if on Monday, you started with a 10GB backup, on Tuesday what would have been 100MBs, it may only back up 20MBs. But, when you look at Tuesday's backup, it will appear to be a 1.1GB full backup and would install as one backup.
10. The best backup program is Backup Assist.
11. It only works on servers. It takes Microsoft's backup software and puts it on steroids.
12. Because it works with Microsoft's VSS writers, it will back up SQL, but if you want the full SQL Server backup, you will need to purchase the license. It does standalone SQL Server backups, which, again, can be daily to one minute. Not to get technical, but the one minute backups are called Transaction Log backups or T-logs. So, any changes are not backed up as physical files but only as logs like notepads. Then for a restore, it takes the logs and points to the data.
13. I agree with Steven. It is 10,000 times more likely for your hard drive to crash, your data to become corrupt or do what I do, screw around with the server too much and crash it, than for a flood or a fire. Besides, if my office burns down, I will likely sit down and cry for days before I even look for my offsite backup.
Do at least backups ten deep. It is mre likely you will lose a file that you need to go back and get than you will just need a complete restore. Remember, the most likely thing to fail in a computer is the hard drive. And, where are your backups? On hard drives.