What are you using to install El Cap? (bootable USB flash drive?) What method did you use to create the bootable flash drive?
The latest DiskMakerX vers 5 does a great job, and gives you an installer that seems more stable (to me)
I would do the format while booted to Yosemite, as I haven't quite got the new Disk Utility that comes with El Cap figured out yet when one needs to control how the partitions are set.
Boot to Yosemite. Your drive that you want to use for El Cap should be in place, too. (Use a different slot this time, unless you have already tried changing to a different slot position.)
Run Disk Utility. Choose your hard drive device line (which has the hard drive information, not the partition), which is usually the first line in the list for that hard drive.
Click the Partition tab. Choose "1 Partition" from the Partition Layout dropdown. Name your hard drive, if you like. The Format should be set for Mac OS Extended (journaled). Also, double-check in Options, that the drive is set for GUID partition table.
Click Apply.
Quit Disk Utility.
Now, boot to your El Cap installer, and install OS X on your newly created partition. Should work.
Hard drive? or SSD? Exactly which drive model are you trying to use?