‘makecert’ is not recognized as an internal or external command in command prompt

The else needs to be on the same "line" ^(a) as the if. Remove the new-line before the else like so:

if "zz"=="TRUE" (
    copy /a zz + /a ee=/a zz
) else (
    copy /a e + /a %TMP%=/a e
)

Please also note that "zz"=="TRUE" will never evaluate to true - I suspect you meant "%zz%"=="TRUE"?

^(a): This isn't always a good description, though it's what the Microsoft documents use. Same command may have been better, and putting ) and else on a different line breaks it into two commands.

Your problem is most likely that the shell does not know where to find your make program. If you want to use it from "anywhere", then you must do this, or else you will need to add the full path each time you want to call it, which is quite cumbersome. For instance:

"c:\program files\gnuwin32\bin\make.exe" option1=thisvalue option2=thatvalue

This is to be taken as an example, it used to look like something like this on XP, I can't say on W7. But gnuwin32 used to provide useful "linux-world" packages for Windows. Check details on your provider for make.

So to avoid entering the path, you can add the path to your PATH environment variable. You will find this easily. To make sure it is registered by the OS, open a console (run cmd.exe) and entering $PATH should give you a list of default pathes. Check that the location of your make program is there.