You have a tough task ahead of you. My suggestion is to plan everything on paper. You need to subnet the flat network, create a VLAN for each of the subnets and then do inter-VLAN routing. Apart from that, you need to have a VLAN for common services like apps servers, DHCP, DNS, etc. which need to be reachable by all VLANs. One VLAN should be kept separate for management/administration purposes. Also, keep in mind scalability requirements...
for the future.
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