Deploying custom scripts

I'm trying to deploy custom package along with a script. Deploying the package is no problem using "call %PATHTOFIXES%Custom_Package.exe" But, using the same method "call %PATHTOFIXES%Custom_script" does not.

Questions:

Can a 'custom_script' run when changing directory outside of 'C:\Windows\ProPatches\Installation\%PATHTOFIXES%'? Meaning use CD C:\Temp as an example.

Can you call a .exe within a sub-directory of %PATHTOFIXES%? For example 'call %PATHTOFIXES%\Folder\application.exe'