What is the best way to construct Java EE application deployment environment on Ubuntu?

What is the best way to construct Java EE application deployment
environment on Ubuntu?

I'm a Java developer and I don't get familiar with Linux especially
Ubuntu. For the past 2 weeks I've worked in transforming our Java EE
appliaction deployed from Windows platform to Ubuntu, including installing
Apahce, tomcat, MySQL, Openfire, JDK,etc through the Ubuntu apt-get
install tool like the command line 'sudo apt-get install tomcat7'. Right
now we found something uncomfortable and unconvenient during maintanence
of the system, for instance, the log files genernated by application or
tomcat cannot be easily found, configuration files and startup files are
dividually put the different folders, we know generally, startup files
will be under /bin and configuation files will be under /etc and the
libraries our project depended are under /lib, etc which are hard to
manage.
So I's thinking if there is a better way to do it just like on Windows,
tomcat to be installed in a individual folder which can be intensively
managed for logs, configuration files, startup files, the answer is yes,
we can install all of these softwares individually, but someone tells me
that its better to use system command line to install tools we may use.
I want to ask if there is a standard claim for that, what is the
difference between 2 ways for installing our tools like tomcat, JDK.