When you get the options on where to install Ubuntu you can chose between installing it alongside Windows, erasing the disk or something else.
Installing it alongside Windows will shrink your Windows partition and create a new one. If you already created one, that isn't detected. So what you want to chose is something else.
Just follow the official instructions on this.
If you already picked the first option you might now have ended up with a Windows partition that is too small to boot. You can fix this by booting the Live-CD/USB to the desktop ("just try Ubuntu, don't install"). Now run gparted to view all your harddrives and partitions. Delete the Ubuntu partitions and resize the Windows partition to the maximum. While you're at it, you can also use gparted to easily create the partitions you need on your second drive (chose it in the top right) and then just select them in the Ubuntu installer.
When manually installing Ubuntu on a second harddrive (/dev/sdb) you probably want the bootloader GRUB to be on the first harddrive (/dev/sda) so make sure your selection looks sound.