Installation Problems and questions

Suppose I have created several partitions on my internal drive by using a answer file, now I would like to have some apps installed on those particular partitions. Do I install them right after I put windows on my reference machine or do I figure out the particular switch such as the next few lines ?

my runonce.bat file:
@ECHO OFF
:START

md D:\APPS\MUSIC\PLAYER
md D:\apps\video\vlc
md E:\Utils\cleaners\crap
md E:\Utils\UNINSTALLER\IOBIT
md E:\Utils\HD\Defrag\
md E:\UTILS\FILE\COPYIERS\
md E:\utils\antiVirus\avast
md E:\utils\AntiMalware\MBAM
md E:\utils\Spyware\SpyBot
md E:\utils\Spyware\SuperAntiSpyware
md D:\APPS\Internet\browsers\firefox
avast_free_antivirus_setup_offline.exe /DIR="E:\UTILS\ANTIVIRUS\AVAST" /VERYSILENT /NO RESTART
iview451_x64_setup.EXE /SILENT /FOLDER="D:\APPS\GRAPHICS\IVEIW"
mb3-setup-consumer-3.4.4.2398-1.0.322-1.0.4470 /register: 4P7B-MGPB-4GVD-3RN7 /DEFAULTDIRNAME=E:\utils\AntiMalware\MBAM
winamp5666_full_all.EXE D:\APPS\MUSIC\PLAYER /S
vlc-3.0.1-win64.EXE /QUIET /S /D=D:\apps\video\vlc
spybot-2.4.exe /DIR="x:\dirname" /VERYSILENT
setup.exe /D=D:\APPS\Internet\Browsers\Firefox /S
ccsetup541.exe /S /E:\UTILS\CLEANER\CRAP
chkdks c:/f/r
chkdsk c:/f/r
:END

where do I tell windows where to look for the runonce file? John

If a picture is worth a 1000 word I thought this picture would help. In this picture it shows the WSIM and 2 arrows , `I am to do what the second one says to do, to run a file called disk maint and apps.cmd using these commands is this possible? What do I put in there?? John