Shinta is right this would be your ideal way…
Im sure you wont go to these lengths with your question but hey here it comes anyways… 
after numerous installs of diffrent versions of windows xp,vista,7 using differnt Motherboards and components.
This is how i just went about my latest builds software and instal…without sounding smug its running sweet!
i have two pcs one for the web and one for audio so prepair first if you only have the one download your motherbord drivers first or at the very least (your LAN one)
unplug/remover all external hardwear e.g motu,usb hdd’s,iloks,elisencer dongel ect
back up all your wanted deta!!!
on start of windows install deleted and re-partition your drives mainly your op system one,dont worries about others.
install windows,
(if your installing windows 7 its best to not let it connect to the web straight away as it will start to look for updates so when it asks if you want to connect choose not at this time) some might argue differnt but this way has always proved better for me.
Then install the latest motherboard drivers from manufactures website.
then enable your LAN and make sure that firewall is active…(should be anyway)
check hardware like dvd writers and hdd/ssd web pages for firmware updates all ok and suport 64bit if thats your op system.
if all good (this bit would prob be the bit your interested in)
turn on windows update and let it do its thing.
I found the most stable way to install updates was to let it download all updates it can then access the setting for auto update and change the shedual time for installing them behind what time it is.i went for 0:00.then it will set itself up to install when you power down the pc.keep repeating this utill no more updates are avalible.this way you will not incounter fails to update and half the time it takes to get them all on!
however you can just keep letting them install while windows is running but your gonna spend double the time doing it!
you should have the latest .net framework and updates…be mindfull you will need other programs like flash and adobie reader silverlight ect…but these can all be found easly.
then move on to your other devices and install one at a time.
start with your motu once its installed dissable your boards onboard audio via device manager and move on.
once all hardware is done i will install cubase/vst’s update progams and sort lisences on vst instruments ect.
then move on to disabling sevices i dont need and cuting of web access
i disable lan in the device manager and blutooth.my pc will not see the web untill i have a problem or need to update things because of one…u may need to keep yours on?
then just config your windows for audio and start testing.you could even try a dsp latency checker to to see how she’s running i like latencymon by resplendence it has more what i need for this…to be honist my system is working that well i have had no need for it this time…could be the spec of it i guess?
their are lots of guides and setup ways avalible on the web.
this way has prooved best for me im not saying that its 100% correct or THE way to do it but im MAJOR fussy about my DAW being in top working order…and it is so hope some of this helps as of couse all pcs are diffrent.
good luck man
