Startup Manager not showing Bootable USB drive
The USB drive should have an EFI partition, which contains files needed to make the drive bootable, in addition to the MacOS formatted partition containing the actual system to boot. The below command should handle all of that for you though.

I have formatted the USB to Mac OS (Extended Journal) and made 1 Partition in the GUID format. I used the file command in Terminal from APPLE (for Yosemite) which all appears to be working. I tested the USB on my 2011 iMAC and can view it on that 'Startup Manager'. However on the MBP 2009 running 'EL Capitan'I am not given the option to boot from.

I'm not sure if the below command is what you refer to here. Running the command in Terminal where you have &quot;Install OS X Yosemite.app&quot; in your applications folder should create a bootable USB drive.
sudo /Applications/Install\ OS\ X\ El\ Capitan.app/Contents/Resources/createinstallmedia --volume '/Volumes/MyVolume' --applicationpath /Applications/Install\ OS\ X\ Yosemite.app
Be sure to replace /Volumes/MyVolume with your USB drive which you can find with ls /Volumes
https://support.apple.com/en-us/HT201372
If you've already tried the above solutions which I assume to have, try resetting the PRAM:

You can reset the pram by doing the following:

Shut down the Mac.
Locate the following four keys: option, command, p and r. You'll need them in the next step.
Power on the Mac, then immediately hold option, command, p and r. You need to do this before the grey screen appears.
Hold down the keys until you hear the startup sound twice, then release them.
Plug in the bootable USB stick, restart the Mac, and hold option.


https://apple.stackexchange.com/a/163327/383607