Drop the switch
Connect the ISP modem to the Primary HAPAC ROUTER.
ensure you have the basic firewall rule set in place.
(https://forum.mikrotik.com/viewtopic.php?t=180838 - see subpara 6)
Read this article.
It covers adding vlans and configuring the MAIN ROUTER as well as setting up the second AP as mainly a accesspoint/switch.
http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1
Give it a whirl and then come back and post both configs
/export hide-sensitive file=anynameyouwish