I suspect there are different ways, with different tools, that folks use for disk cleanup/maintenance/repairs, and backups. I can explain what I do, along with "associated" alternatives. So, here goes.
First, for backups, there are two types that can be made: either bootable or non-bootable. For non-bootable backups, Time Machine is the way to go. It is free, and comes as part of the Mac OS. For bootable backups, there are two excellent products available: SuperDuper! (I use that one; costs $27.95 US), or Carbon Copy Cloner (costs $39.95 US). Either of them make an exact copy/bootable clone of your system to the external device. It's just like having an "extra" computer. The difference between the two is that Carbon Copy Cloner backs up the (hidden) Recovery HD partition created by an installation of the Mac OS, whereas SuperDuper! does not. But, that is not an issue for me, as 1) I use two excellent, venerable products for disk cleanup/maintenance/repairs, and 2) it can be easily re-created. Recovery is much easier via a clone, and one can boot/re-boot their machine from the clone, and use all the tools there for recovery. With a Time Machine backup, one must first boot to the Recovery HD partition, and then go through a longer (and to me a somewhat more "complicated") process to do the recovery. But, there are many folks who swear by a Time Machine backup, and that's all well and good. As the old saying goes, "To each his/her own".
Next, for disk cleanup/maintenance/repairs, here is what I do:
1. I use Outlook for my EMail needs, and when an I delete an EMail, it actually does not get physically deleted from my SSD. So, when I start my weekly disk cleanup/maintenance/repair, and backup processing, I use a Microsoft-supplied method of having such "deleted" EMails permanently removed. I suspect something similar could be done with other EMail software.
2. I next run the excellent freeware program Onyx. This venerable gem has been around quite a while, has excellent reviews, and works very well. In fact, I will not upgrade the Mac OS until a compatible version of Onyx is ready. That is how much I depend on it. I use it to 1) Repair Permissions, and 2) do some disk cleanup/maintenance. The Repair Permissions feature is still useful (at least for me), even though the Mac OS (since El Capitan) supposedly repairs permissions, but every time I use Onyx to perform this function on both of my Macs, it certainly does some repairs.
3. Then, I use the excellent program TechTool Pro for more extensive disk maintenance/repairs. Again, this product has been around for a long, long time, has had excellent reviews, and works well. And, just like Onyx, I will not upgrade the Mac OS until a compatible version has been released. In fact, that is the exact situation now. Micromat (the company that develops TechTool Pro) has not yet released a version compatible with OS 10.12, Sierra, and thus I have yet to upgrade the OS.
4. Finally, I run SuperDuper! to do a backup/clone of each of my Macs to two separate external devices.
While this process may appear to be time consuming, I am actually doing other tasks while this is going on. A number of the processes take some time, and thus do not need to be monitored.
For Onyx, there are two other excellent (and similar) products available: Coctail, and Tinker Tool. (I suspect there are others also). But, I have been using Onyx for so, so long, with continued success.
For TechTool Pro, the other two products are Disk Warrior, and Drive Genius. Disk Warrior is especially notable, as there are times when it can do "wonders". But, it does not have as many features as TechTool Pro does. Yet, it is an excellent, excellent product.
One other thing is that Disk Utility can also perform "some" of the disk cleanup/maintenance/repairs, but not as effectively as the products I mentioned above. Also, to perform such functions, it is necessary to first boot/re-boot your machine to the (hidden) Recovery HD partition I mentioned above.
Finally, I am actually doing disk cleanup on a daily basis. Besides EMails, there are times where I delete prior versions of software, which happens whenever a newer version comes out.