As long as your IP addresses are well defined you may not have any collisions, but a good approach may be using subnet masks and ACLs on the router so that traffic from one subnet has no access to traffic of the other subnet. I only know how to configure ACLs on cisco routers so if it's another brand I can't help you very much. But subnetting can be used on (almost) any router, you just have to set up your network like this:
Subnet A
Gateway: 192.168.1.127 and subnet 255.255.255.128
Only IPs in the range of .1 up to .127 will have direct access between them.
Subnet B
Gateway: 192.168.1.254 and subnet 255.255.255.128
Likewise, only IPs in the range of .129 up to .254 will have direct access between them.
If any computer inside Subnet A wants to communicate with any computer inside the Subnet B they'll have to pass through the router, and that's where ACLs come into action, they may block or let access for certain IPs or block any IP of a certain subnet completely.
Of course the swicthes must connect to different ethernet ports of the router (each one is the respective gateway for each subnet, the router must let you specify an IP address for each port), otherwise you must implement VLANs and use a trunk port to connect.
I'm a little too rusty now regarding networking but I hope this helps you.
Good luck.