No Problem....
When you are using VLANS, you're basically sending several subnets down the same cable/segment. VLANS are completely separate and discreet information flows (broadcast domains). Like any net-to-net or subnet-to-subnet communication, the only way to get information from one VLAN to another is to route it.
Since you are basically only running one cable to the router (with multiple VLANs on that cable), it was termed a "One Arm Router" (actually a term that came from the ol' ATM days with ELAN to ELAN routing). Cisco likes to call it "Router on a stick" because the Cisco Icon is a circle, and the line drwan up to it makes it look like a lollipop (on paper).
A router acting as a "one arm router" can (usually does) support other connections at the same time, but for the purposes of discussion, it's usually talked about as one trunked connection to the router (packets come in on one VLAN, and leave on another, but stay on the same trunked connection). Packets can be routed from a VLAN on the trunk to other trunks or discreet subnets.
My comment about using an 802.1q or ISL NIC in the server is sort of the same thing. When you install and configure a VLAN-enabled NIC in the server, you install a single PHYSICAL NIC. When you enable 802.1q or ISL on that NIC, the drivers make it appear as multiple LOGICAL NICS, one for each VLAN you define. The effect is that you have (for example) four physical connections going to four physical NICs in the server .... making the server appear as a local host on that subnet / VLAN (the ideal setup is zero-hop to the resource, if possible).
MLS is Cisco-speak for "Multi-Layer Switching." With the proper router/switch combination, a packet needing to cross VLANs (needs to be routed) is sent from the switch to the designated router for routing. The switch keeps track of the packet to see where it came from, and where it's going. When it comes back from the router, the switch confirms the destination, then places all the information in a table (CAM).
The next time a packet from the same source going to the same destination comes into the switch, instead of sending it to a (slow) router, it just changes what needs to be changed, and switches it on to the destination ... much faster (wire speed) than routing. There are several variations, but the basic premise is "Route the first packet, switch the rest." The process can be cranked down to where a packet from the same source, same destination, same socket/port (a packet port, like 23 = telnet) get's it's own entry in the CAM. It can also be "loosened up" to the point where any packet from the same source going to the same destination gets an entry. A threshold can be set so that infrequent flows do not get MLS switched.
Graphics would help a lot. If it's still not clear, check out MLS at Cisco's web site.
FWIW
Scott