Unfortunately, Time Capsule won't back up your Windows partition. You'd have to do that separately.
I'd suggest using a program like Crashplan to backup your entire Windows hard drive to an external HDD (free with Crashplan). Then format and/or restore you Mac OS X hard drive from Time Capsule without changing the partitions, and finally format and/or restore your Windows partition from the Crashplan backup.
Of course, Windows being Windows, needing a format every now and then (yes, I'm prejudiced) and not having a proper "restore entire OS from backup" option like Mac OS X, an easier road might just be to backup the actual important data of your Windows partition, like documents and application preferences, onto an external hard drive, and to then format the partition and install a fresh copy of Windows to which you copy your important stuff. That's probably what I would do.