The safest way to manually install the service is to use the provided service.bat script.

Install the service named ’Tomcat5’
C:’> service.bat install

If using tomcat5.exe, you need to use the //IS// parameter.
void void 
Install the service named ’Tomcat5’
C:’> tomcat5 //IS//Tomcat5 --DisplayName="Apache Tomcat 5" ’
C:’> --Install="C:’Program Files’Tomcat’bin’tomcat5.exe" --Jvm=auto ’
C:’> --StartMode=jvm --StopMode=jvm ’
C:’> --StartClass=org.apache.catalina.startup.Bootstrap --StartParams=start ’
C:’> --StopClass=org.apache.catalina.startup.Bootstrap --StopParams=stop
To update the service parameters, you need to use the //US// parameter. 
Update the service named ’Tomcat6
C:’> tomcat6 //US//Tomcat6 --Description="Apache Tomcat Server - http://tomcat.apache.org/ " ’
C:’> --Startup=auto --Classpath=%JAVA_HOME%’lib’tools.jar;%CATALINA_HOME%’bin’bootstrap.jar

To remove the service, you need to use the //DS// parameter.
If the service is running it will be stopped and then deleted. 
Remove the service named ’Tomcat6’
C:’> tomcat6 //DS//Tomcat6

This is an extract from

http://tomcat.apache.org/tomcat-5.5-doc/windows-service-howto.html