Nate,
Let's take these one at a time as it should be helpful for everyone. And, hopefully, they will be helpful and you won't take them critically.
1. Hard drive space. There are a lot of programs which are supposedly designed to help you with your software and hardware. MOST are crap. CCleaner can be a good program to help with temp files, etc. On a CLIENT, it can clean up a lot of space. You would never use any registry cleaner on an actual server. But, it's a good idea to at least be familiar with your server whether it be your "main computer" or actual server. For instance, at the moment, I have 120GB out of 250GBs on my server. I may check that every two weeks or so, but for them most part, I will just have it memorized. Remember, everyone talks about RAM and processor speed and HDD/SSD speed, but your performance will diminish appreciably if your get down to too little space. One thing which can take up a lot of space is updates. But, not many people even use anywhere near a 400GB hard drive (although they have gotten quite big lately) but to run your OS and programs and your Active Directory for the most part, you won't need nearly that much. Given that is almost twice the size of my C: drive, I would have been getting warnings left and right way before AC ever remoted in. Once nice little program is called Treesize Professional. Now this is generally after you realize a problem exists. But, if I noticed 400GBs, I would have no idea where to start, but if I ran Treesize (as it sounds) it puts your folder structure from large to small. So your Program Files would be rather close to the top and then you would see AC with 400GBs and, hopefully, you would be like "holy..." My biggest issues besides temp files is a couple of times a full backup got stored in the C drive. Don't know how, but that was a 15GB backup drive that was supposed to be headed toward a 1.5 TB backup.
2. 400GBs in your backup folder. Why? Because AC has the Microsoft gene. They think many wouldn't know about backups, so the default backup gets put right in the AC folder in a folder called BACKUP. Now, I can name one reason right now why that may be a good idea, but you should be able to turn it off. Now, I am going to guess when you open up your backup program for AC, there are three extra paths, and they may be normal. The first thing you want to do is make a backup path for off your computer.
As far as the backups in the backup folder, you can either remember they are there and manually delete them. Or there are programs that will do that based on how many or the date. Or you can use a script in a bat file such as:
forfiles /p "D:\Amazing Charts\BACKUP" /s /m *.* /c "cmd /c Del @path" /D -3
You copy and paste this in a notepad.txt file and then rename it notepad.bat. Well, you would probably want to rename it Remove.bat or RemoveACbus.bat. Once you do this, is will delete the last three files based on modified date. So you can just click on that every so often.
3. Now, why this isn't located on the backup window, I will never know. But, it is located in the Administrative Options. Main window then click on CTRL + A. This will open the admin options window. You can also go there via View | Administrative Options. Once there, on the bottom right, go to:
Miscellaneous preferences and and tick the fourth box from the top so that it disables Overdue Backup alerts.
I am different from the other 8,500 users. Well, I am different than most. Obviously, you can schedule your AC backups. I have three major programs I HAVE to run EVERY night. That is AC backup, Files backup and my Medware backup. I do run a quick incremental off the server that takes about 15 minutes. So, I finish patients, run that incremental backup while I am working. And, when I go home, I can start the three modular backups. I generally can see that they are done, etc.