It's not terrible backing up a system while running. However, it's not optimal, if you have the option to backup after a clean shutdown.
When a system is backed up during operation, the backup system connects to the OS, and listens for writes to the drive. As the backup proceeds, anytime the OS attempts to write to a sector on the source drive, the backup software intercepts the write; that sector is then backed up immediately (out of normal order), before the OS is allowed to overwrite it.
The backup therefore contains an exact snapshot of the drive at the instant that the backup started.
If you restore from that backup, it will be as if the power had gone out at the instant that the backup started. When the OS boots, it will have to do its "unexpected shutdown" clean-up.