There are two ways of having multiple instance of tomcat on Windows OS.
Independent binary distribution
This is the easiest way. You need to have two binary distribution of Tomcat. Change the port's in conf/server.xml used by Tomcat so that instances don't conflict each other at startup. The example of ports are
Server port="8006", Connector port="8081" Connector port="8009" for Coyote/JK2 AJP 1.3
For this You need to have CATALINA_BASE (for eg set CATALINA_BASE=D:\catalina1) set as environment variable and put conf, webapps, logs, work folders under CATALINA_BASE(D:\catalina1). Change the port in CATALINA_BASE\conf\server.xml. Now install this as windows service by executing
jakarta-tomcat-5.0.28\bin\service.bat install TomcatCustomised
The http request for this instance is served from custom port.
Now set CATALINA_BASE=%CATALINA_HOME% and install second instance
jakarta-tomcat-5.0.28\bin\service.bat install Tomcat5
The http request for this instance is served from default 8080 port.
More information on starting and stoping service at http://jakarta.apache.org/tomcat/tomcat-5.5-doc/windows-service-howto.html