How to manage secure networks when multiple networks are available and can create conflict. i.e. Wi-Fi Network, Wired Network, Optic Fiber?

 What type of switch? if it is layer 2 switch, it is require a router before the two devices on different VLANs can communicate with each other. Layer 2 switch cannot route between VLANs except with the help of router.   But if it is layer 3 switch, then the switch has router built in and it can route between VLANS without router.  Then enable inter-vlan routing.

i am not sure exactly what you mean

but if you mean you have same subnets used on different networks which you need to connect together

then your answer is NAT or site to site VPN depending on the geographical location of the networks