when to use "server.startup.bat"(../JazzTeamServer\server) and "startup.bat"(../JazzTeamServer\server\tomcat\bin)?

startup.bat is the one which starts the tomcat application server by calling catalina.bat

startup.bat is used by server.startup.bat after setting the environment with proper heap (xmx, xms .. ), garbage collection policy (gencon...), the jdbc dirvers to use, log configuration to use and other things which define the run time environment for applications.

server.startup.bat [ setting the runtime ] >> startup.bat >> catalina.bat [ app server starts ]

you can open these files in a text editor to get a complete view of what settings are managed through and the invocation order as well.

In most cases you should use the one from "JazzTeamServer\server"