I have downloaded onto a flash drive. It shows in disk utility..... what do i need to do now to reinstall OS El Capitan to factory settings?

How to get old versions of macOS Read the full details.

How to create a bootable installer for macOS and note: The commands to create the USB Installer must be executed from an Apple Compatible computer to Create the Bootable Installer.

And if you download this file " I have downloaded the El Capitan settings onto a flash drive via my laptop using windows." this is NOT A FULL INSTALLER of El Capitan

The full installer of El Capitan can Only Be Downloaded from an Apple Computer that Qualifies to Run El Capitan

How to erase an Intel-based Mac as per Apple Instructions

How to reinstall macOS also from Apple Instructions

The two above will basically put the computer back to Factory Setting and reinstall the OS as per the version associated with the Recovery Volume on the computer.

You really need to create a bootable USB flash drive using another mac,

trying to do it on Windows machine is not recommended, it don't work.

If you can borrow a mac that you know is capable of running El Capitan you can do this.

Click on the link below,

How to get old versions of macOS – Apple Support

Go to Download OS and click on OS X El Capitan 10.11

this downloads InstallMacOSX.dmg to your Downloads folder.

The next section can only be done on a mac that is capable of running El Capitan.

This includes macs that have the potential to run El Capitan but have been upgraded to a newer OS.

A mac that came preinstalled with an OS later than El Capitan will refuse to do the next bit.

When downloaded open to InstallMacOSX.pkg, double-click on

that and an installation window will open, this does not install El Capitan

but converts the InstallMacOSX.pkg to the Install OS X El Capitan.app which 

you will find in your Applications folder, it should be 6.2GBs in size.

(If the installation window asks which disk you want to install to, you must pick 

the disk that you are booted to at the time. Not any internal or external disk that 

you want to eventually install El Capitan on, that is for later.)

To start the installation of El Capitan double click on the Install OS X El Capitan.app.

Create a bootable USB installer disk using the Install OS X El Capitan.app in the Applications 

folder and the createinstallmedia command in the Terminal app. 

Read the instructions here,

How to create a bootable installer for macOS – Apple Support

Use wrote " Possibly because my Apple ID is not the original ID " there is your answer. Purchases from not Original Apple ID are not associated with the previous purchases. Only purchases from the Original Apple ID will work.

User wrote " I have downloaded the El Capitan settings onto a flash drive via my laptop using windows. I have checked the file folders and the files are there." that is NT A FULL INSTALLER if as you stated from a Windows Computer.The Full Installer of El Capitan can ONLY be downloaded from Apple Store using an Apple Computer.

What you may have downloaded is an update for El Capitan. That is Not the Full Version of El Capitan.

Follow these instructions to create an El Capitan USB installer on a newer version of macOS:

https://apple.stackexchange.com/questions/379603/how-do-i-create-el-capitan-installer-on-a-catalina-or-post-el-capitan-installe/388508#388508

If you are going to include that link to the workaround

you should explain that this is for macs that came preinstalled with a newer OS than El Capitan.

Macs that can run El Capitan but have been upgraded to newer OS's can still do the conversion

without the need for the workaround in the link you posted.

What have you downloaded to a flash drive?

Did you use the instructions here to create your bootable USB flash drive,

How to create a bootable installer for macOS – Apple Support (UK)