Help with IP Subnetting/VLANS

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Ok, here it goes:

I have a network with about 40 servers in it. These serves are currently on a flat lan where they are all addressed out of 3 IP blocks provided to me by my upstream. In this network I have 4 edge of network switches and one center distribution switch. Recently, I was able to upgrade to add a router to our network so now we have a Cisco 3550-12T with IP Services in front of the distribution switch.

So now that I have routing in place I need to subnet out my network so that each server gets its own IP block rather then using random IP addresses from the larger IP pool. I have a full /24 I can break up to start the process of moving the servers over to the fresh IP blocks. Once some are moved over I can renumber some of the IPs in the other blocks and return any that are not needed.

My question is how do I go about doing this exactly? I understand how subnetting works and I have a pretty good grasp of what a VLAN is but everywhere I read (and I checked at least a dozen books) just goes into how subnetting works and what a VLAN is but does not provide me with the commands I need to enter and what kind of VLAN design options I have. I understand that I should be using VLAN trunking and that I don't need to assign each server with a VLAN but then I don't understand how you can assign each host an IP block and keep anyone else from using it...

Does anyone understand what I am asking?