Use Iptables as only a gateway firewall

I am a true beginner to Linux and IPTables... I am working for a
startup and their previous admin had set up iptables, NAT, and DHCP and
who knows what else on a Linux box. He had mentioned to me that all
traffic even internal passes through the IPtables. I have a Layer 3
switch that can route instead of using the Linux firewall. I would
like the IPtables to be soley used as a true gateway firewall.
The virtual interfaces for the VLAN's are all set up as is the DHCP
with their appropriate subnet gatway addresses. With that said, things
work fine right now, but the internal network tends to get real slow at
times. I want to connect the three layer2 switches to the layer 3 and
use that to route between VLAN subnets. How would I go about setting
this up? Thanks.