I managed to figure this out and thought i'd share in case anyone else has this issue.
I was massively overcomplicating the process and it turned out to be quite easy to get working.
Added to extra formatting steps in the task sequence so it looks like this:
for UEFI booting
300 MB (Windows RE Tools) NTFS
512MB (EFI) FAT32
128MB (MSR) MSR
200GB for OD, NTFS
50% for 1st VHD, NTFS
100% for 2nd VHD, NTFS
Then after the "Setup Windows and ConfigMgr" step.
Connect to the file share with the VHDS ( Connect to Network Folder)
Copy the VHDs to each partition using robocopy (Run Command Line)
And then i used a scrpt found here: https://blogs.technet.microsoft.com/danstolts/2011/03/how-to-automatically-create-bcdedit-data-for-a-boot2vhd-file-on-your-windows-7-or-windows-server-2008-r2-machine/ to Add the entries into the boot menu and also rename.
I created a package with source files, and added the script into there and then used a Run Command Line step to call the script and rename and add the boot entries
Hope that helps anyone else with this issue.