3rd access point? I thought you are just going to repurpose your spare access point as secondary. Anyway, yung setup 1 sa diagram is if you are going to use the 3-in-1 supplied by ISP. Yung 2nd diagram is if you have a specialized, custom router like pfSense, mikrotik or any Linux/BSD-based router.
And to further clarify, sa fibre net yung ONU/ONT, hindi pa iyan modem nor router. It's an optical device that converts optical signal into electrical. Yung ikinakabit mo dun, yung yung 3-in-1 (modem-router-switch functions rolled into 1). That is almost always crappy.
Assuming that you already know basic IP subnets (/24, /16) so that you don't mixed them up, ang systematic troubleshooting, if you are unsure, check the connectivity of a node to its gateway first. You have to check its connectivity to its gateway's IP first. Disregard hostname resolution at this stage as you don't need DNS yet. You can use various tools to do that. In Linux, you can use ping, tcpdump, wireshark, ip, arp etc. Sa Windows, you can use ping, netstat, wireshark, arp; then check the next hop router so on and so forth...
Going back to your setup, what's the IP addressing of your 2ndary and tertiary router/AP? Magumpisa ka mag-troubleshoot dyan, papunta sa main gateway. That is assuming may router-mode yung 2 access points/routers mo.