dear lax,
                pl bear with me.this is going to be a long i understand it u r having two databases( say oracle & sql-server) serving two diff applications(i.e each has it's own jsp's and servlets).now one way to do it is create two different contexts of tomcat and create WEB-INF and  examples/jsp folders for each context.then u can simply put the respective applications in each context and happily run them and no need for the ini file to have the dsn's .u can create the dsn's in ODBC datasources wizard in administrative tools(win nt) and use url="jdbc:odbc:<dsn name>" .but this way ur performance is poor(as there is only one jvm is being used by tomcat).what u can do is read the file "tomcat user guide:a minimalistic approach" in docs dir.u can have two context's using diff jvm's to serve ur takes up sys resources but ur speed improves.the baseline is instead of one server.xml file u need to have two server.xml one xml file u load one context and in the other u load the other context.u can then start two tomcat's by startup -f <path to server.xml>.ur apache then sends the necessary servlet/jsp to the respective context depending upon ur ACTION attribute.
both context's should have diff ports(say 8007 & 8009)
http://localhost:8080/context1  directs to one context
http://localhost:8080/context2 directs to the other context
u need to read the docs is difficult to acheive but not impoosible and should be attempted only if there is real need for it!!!