Mklink and software installation

Hello all,
I'm using mklink to put the installed software on the D:\, that is installed on c:\program files or programfiles(x86). In order to do this I have created (2) batch files. One for mklink and one for installation of programs. Now where do I use mklinkand use to install the programs. Do I use mklink before the setup of a program or after?

John

If I have a program that installs in programfiles(x86)\fred and I use mklink to install it on d:\apps\john\fred.
Would I the programs setup file like this
Mklink
Setup.exe
Or
Setup
Mklink

Not really the site didn't give the answer I wanted . Thank you , John