On a single controller system, the location of the spares doesn't matter at all, so when disks are added to an aggregate, it doesn't try to prevent this.
You can manually place them by first connecting to the system's CLI, turning off auto-assign of disks or shelves, then plugging the new shelf in, then running the command to add new disks to the aggregate with the CLI, manually specifying which disks to use, then turning auto-assign back on.
Exact commands depend on ontap version and clustered ontap or 7 mode.
If you wish to change the existing system, disk movement is supported - you can turn the system off and swap disk locations, or you can use the "disk replace" command to replace an aggregate disk with a spare, then zero the now-spare, former aggregate disk.