This might have been obvious to all you established logparser users but maybe I'm just stupid, anyway I fathomed it out so if anyone's remotely interested this is what you do.
Within your vbscript you will have to write a small function to enable the setting of environment variables, you will do this by using the windows shell, and environment as follows:
Dim objShell
Dim objEnv
Set objShell = WScript.CreateObject("WScript.Shell")
Set objEnv = objShell.Environment("Process")
objEnv(key) = val
Set objShell = Nothing
Set objEnv = Nothing
Now you can just reference the environment variable(s) in your template(s) as normal, hope this helps someone out.
Oh btw to unset the variable you would set up the shell & environment as per the function abaove and call objEnv.Remove(key) instead