Sure. Choose 1 drive to be the Main Boot (C
drive - if either is an SSD, make it that one. Make sure all your DATA (not programs) is backed up and download all the latest motherboard/chipset/usb/video drivers
1- install into computer only that drive u want to use for C: and only have a keyboard and mouse connected - no other peripherals
FRESH install windows on the drive, after deleting all partitions
2- when at windows desktop for the 1st time, install motherboard drivers, chipset drivers, usb drivers, in that order - reboot - run windows update at least 3 times (rebooting after each time)
3- then install video drivers (ONLY if you have a video card inserted in a slot in the motherboard) windows update would've covered the on-board drivers, don't let it install drivers if you have a card
4- then install the other hard drive
now u have to install every program you want to run, but you can choose where to install it - the new C: drive or the data (E
drive