Converting to an answer to address piecemeal.
We have bought a "Redhat Enterprise Linux 5 Server" license
Red Hat doesn't use licensing, it uses an entitlement system for managing sales.
You buy access for x number of nodes for a particular base channel. The base channels are specific to a particular RHEL version (such as "rhel6-x86_64" or "rhel5-i386"). You would have to contact Red Hat (as Mat suggested) to see if they have the ability to transfer entitlements between base channels. Assuming the prices are the same I don't see why not, it's just a question of what their company policy is.
Does the license limit number of servers that can be installed or the performance of a server (Like oracle)?
The number of entitlements will restrict the number of systems you can subscribe to a channel on either RHN Hosted or any local Satellite you may have (which doesn't sound like you would have). When you run out of entitlements, you just lose the ability to subscribe the system.
can we use our installation number to create support account, we have never created one?
Installation numbers are for the individual systems. You'll want your account number, which should be on the documentation that was sent to you when you purchased your entitlement.
Personally, if I were in your position, I'd just install RHEL6 (which you are allowed to do) and just work out the entitlement issue on the backend with the intentional of subscribing the system for updates when you have an entitlement available on the RHEL6 channel.