If you can put AP on same subnet as controller to configure its easy:
1. place UniFi controller in the desired subnet, you need to give it static IP (or statically assigned-IP through DHCP)
2. place APs in the same L2 so they're adopted
3. move APs to their desired subnets
4. as APs know where the controller is, they'll phone home
If you cant connect to same subnet first then you can configure using Unifi discovery tool or SSH
To use Unifi discovery tool follow instructions on this video:
https://www.youtube.com/watch?v=nFN5N7P0JQE
Alternative approach: (SSH required)
1. Use DHCP to determine IP address
2. Connect via SSH to UniFi
3. Log in as ubnt pw ubnt
4. type "set-default"
5. wait for reboot
6. Connect via SSH to UniFi
7. Log in as ubnt pw ubnt
8. type "set-inform http://192.168.0.2:8080/inform" where 192.168.0.2 is the address of the controller
9. Adopt the unifi in the controller and set the ip address and subnet mask
10. type "set-inform http://192.168.0.2:8080/inform" where 192.168.0.2 is the address of the controller (AGAIN)
11. wait for reboot
12. Should now be adopted.