Restoring two partitions from Time Machine

If I use the "Restore from a Time Machine Backup" routine (from my Recovery HD on a USB stick), will it automatically recreate and populate the two partitions as they existed before?

No.

If not, what process should I follow to make that happen?

Partition the drive as you wish, then restore the startup volume to one of the partitions. If you have two bootable volumes, you can restore the other one the same way. If the second partition holds only data, restore it in the time-travel view after booting from the volume you've already restored. Note that you must select the destination by right-clicking or control-clicking the icon of the volume to be restored and selecting Restore to... from the contextual menu. Also note that if you want file permissions to be preserved, you must first open the Info window of the volume in the Finder and uncheck the box labeled Ignore ownership on this volume.