Hello,
Zoiper should be automatically started in background on iOS after reboot of the device only if it was already started at the time of the reboot.
Otherwise for using Zoiper in background, it is best to use TCP or TLS transport (your VoIP provider must support these as well, or your account will not register), since UDP is not reliable on iOS. The changes of the transport type can be done from the Network Settings menu in the account configuration.
Make sure that you also have enabled all the notifications in the "Notifications" menu from the iOS Settings menu.