One common issue we see, particularly from customers familiar with Project Server 2003 is that they will install WSS v3 before Project Server 2007. This is an unnecessary step and in some cases can then make it difficult to install Project Server 2007 in precisely the way that you want. For instance if WSS is installed then it can install a SQL Express instance for its databases. Then when you install Project Server it follows the lead of WSS and also uses SQL Express - when you really wanted to load the databases in another instance of SQL Server 2005. Just installing Project Server 2007 will also install all the bits of WSS you need and allows either a "standalone" install - which does use SQL Express, or you can choose "Advanced", followed by "Complete" and this will allow a choice of SQL Servers to connect to. Often a customer will choose standalone to mean that SQL will be on the same server - but will not intend to use SQL Express - but a full SQL Server 2005 database engine that is also running on the server. Standalone does not give you the choices - but Advanced and then Complete does.
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