Don't confuse things.
Windows server COULD do RAID but if you can, DON'T do a software raid! It's sloooow, really slow. Use your raid controller. This will be configured after the POST and before the Windows installation. I don't want to believe that your controller cannot manage 2 differents RAID. Today I have installed a server with 3 RAID on a HP which is really old (7 years) so...
Said that, once you are able to configure your controller, install windows on first RAID and once ready to install create just one partition for WINDOWS (let's say 200 gb) you can adjust this value based on your needs. Once installed, create others partitions (mail, db, webApp) so you will have 4 parts on your FIRST hard drive. Having multiple partitions has (no) drawbacks, but has advantages (one is that when you want to move something maybe on a storage in the future, you can do this easier than with a single confused partition), another advantage... let's say that something screw up your C:\ partition. You have an image of 1 month ago, with a single partition you must restore the image and THEN recover the database backup (and if you don't know... recovery a database no matter if it's sql, mysql, ... it's a BEAUTIFUL job... do it one time for test... you will see when partials records are not recovered... or tables weren't close... beautiful...), so finally you spent one day to recover the system and people cannot work.
With multiple partitions you must restore the old image and windows starts up and the DB file is up to date. You (maybe) must do just some adjustment on your "old" windows.
In the worst case you can simply reinstall a fresh windows server (30-40 mins?) and install your DB software but data is still available! Just a quick thing, if you use shared storage (san, nas) you can map each partition on a host of your choice so you really have a great no-downtime! (Almost
)
Back to you, you have your part (windows), now you can create the others partitions based on your needs.
Finally you have the second RAID ready to "host" your web app database. Also in this case... if you have a db which is 100 gb create a partition of 200 or 250 gb but DON'T use the entire disk. It's EASIER to grow a partition instead of stretch it. Trust me
With windows you can expand partitions but not stretch.
I wrote too much? mhhh maybe