1. You can use them at the same time, RT-BE88U has two 10G ports, one 10G RJ45 port, one 10G SFP+ port.
2. You can use one as WAN port and the other as LAN port. The tech spec says the 10G SFP+ port is for WAN port but in reality you can use it as LAN port based on the reports (same for Asus RT-AX89X).
https://www.asus.com/sg/networking-iot-servers/wifi-routers/asus-gaming-routers/rt-be88u/techspec/
Reference: RT-BE88U 10G SFP+ port can be used as LAN port
https://www.snbforums.com/threads/r...-nat-possible-with-asus-stock-firmware.91423/
3. You can use the 10G SFP+ port as WAN and the 10G RJ45 port as LAN.
ONT --> RT-BE88U 10G SFP+ Port with 10G SFP+ RJ45 module as WAN
10G RJ45 port as LAN port --> 10G switch with RJ45 ports and/or Desktop/Laptop with 10G RJ45 network adapter
3. You can also use the 10G RJ45 port as WAN port to connect to the ONT. Then you use the 10G SFP+ port as LAN port.
ONT --> RT-BE88U 10G RJ45 port as WAN
10G SFP+ LAN port with SFP+ 10G RJ45 module --> 10G switch with RJ45 ports and/or Desktop/Laptop with 10G RJ45 network adapter
Or
10G SFP+ LAN port --> DAC cable --> 10G switch with SFP+ ports and or Desktop with 10G SFP+ network adapter
Or
10G SFP+ LAN port with SFP+ optic module --> Fibre Cable --> 10G switch with SFP+ ports and or Desktop with 10G SFP+ network adapter, with SFP+ optic module
4. 10G switch with SFP+ ports are much cheaper than 10G switch with RJ45 ports.