To get started, you can use the freeware version of SuperDuper! to backup your current system. You can get it from here:
http://www.macupdate.com/app/mac/13803/superduper
Don't worry about the dollar figure. Just click on the download link.
Once you install and run SuperDuper!, it will make a
bootable backup/exact clone of everything on your internal drive to wherever on your external drive you designate (I suggest you make a separate partition on your external drive) . Once you do that (make sure you still have the "Install OS X Yosemite" file, and make another copy of it outside the Applications folder), you can boot your Mac from that partition (will boot into El Capitan). Then, you can run Disk Utility from there to Erase, Format, and (if necessary) partition your internal drive. You can then launch the "Install OS X Yosemite" file from that (still booted into) partition, and install it on your internal drive. You'll thus have a fresh, "virgin" OS 10.10.5 OS on your internal drive.
Once that is done, boot your Mac (should boot from your internal drive), then go to the Utilities folder inside the Applications folder, and launch Migration Assistant. You can then "migrate", ie copy, all the non-Apple stuff from that SuperDuper! partition to your internal drive. You'll then be back in business.
I am holding off on installing El Capitan (already downloaded to both of my machines), as there are at least 2 third party programs that have not been upgraded yet: Onyx, and TechTool Pro. I absolutely depend upon both of those programs.
Just out of curiosity, do you have Quicken 2007, and if you do, does it work OK with OS 10.11? No matter how much digging around I do, I cannot find any place that says definitively whether it is compatible or not. Just about all of the links (including Intuit's site) talk about Quicken Essentials, and Quicken 2015. But, nothing, nada about Quicken 2007.