On your question about running SQL 2000 and 2005 on the same box, the answer is yes, you can do that. And for setting the instance to use only one processor, the answer is also yes.
Just to clarify, you have one SQL 2000 license and 1 SQL 2005 license, right ? and you want to have SQL 2000 and SQL 2005 up and running ? Well, based on the server I'm guessing you have and (only 2 procs), your applications will run slowly specially if you only let SQL use 1 proc... Of course, this is just a performance thing...
To accomplish this in SQL 2005, open SQL Server Management Studio, right click the instance and click on Properties. Then, on the Server Properties page, go to Processors, uncheck "Automatically set processor..." and "Automatically set I/O..." and the just uncheck the 2nd processor. I don't have a SQL 2000 instance installed, so I cannot tell you the setp-by-step with the exact words, but it's similar to this. You open Enterprise Manager, right click on the instance, properties and then search the processor affinity there.
Hope this helps,