iCloud will only backup certain things to backup your whole computer I suggest you get and external drive and use the built in Time Machine backup to get a full backup before upgrading. Then there are no issues with upgrading straight to El Capitan if you make certain precautions first:
Click on the first icon in the Dock (the list of icons at the bottom of your screen) which is the “face” the "Finder", then click on Go at the top of the screen, you will see a drop down menu, go to Utilities. When that opens double click on the application called Disk Utility. When Disk Utility opens you will see your hard drive (usually Macintosh HD) on the left. Highlight your hard drive and on the right select the First Aid tab if it is not already selected, then click on Verify Disk on the far right. If that is OK in green type, then click on Repair Disk Permissions on the left.
Note: If Verify Disk is not OK try to Repair. If Repair is successful then Repair Disk Permissions if it is not successful let me know.