How do I choose the disk to install macOS Sierra?
I don't know how good this may work, but once you boot into recovery mode, from the menu bar on the top, under Utilities you should find Disk Utility. Once you open disk utility, select the disk you want to install the OS on, and then click the Mount option, this should give you a prompt to provide the password to unlock the drive. 

Once you have successfully unlocked and mounted the drive, quit Disk Utilities, and the default window with the option to install macOS should come back, from thereon you may continue with the installation as usual.

I didn't have the opportunity to boot in Recovery mode and make sure this works, so your milage may vary. Also, I would highly suggest you take a look at the guide posted by one of the comments, as well as make a back up of everything important in that drive before you proceed with this! Good luck!