How do I restore a Time Machine backup after repartitioning the original drive? My goal is to backup my data by Time Machine, perform a clean install of Yosemite, partition the disk and restore some of the data. 

Right now my setup is only one partition. After a new setup I want to have two partitions.

Does Time Machine deal with that smoothly though the new partitions have new UUIDs then?
If you restore via time machine (using Migration Assistant or Setup), then it will start backing up to the TM drive like before you restored. Not sure what you mean by if there should be a partitioned disk, as all disks have to be partitioned before you can use it.