I have a question about Software Architecture, anyone can help me or give me some hints currently, I have a J2EE project which deploys in a server, I should a Java Standard project(J2SE) should run 24 hours x 7 days to monitor something

it could not run separately, because the Java Project shared the some same classes such as Java Bean classes with the J2EE project

maybe my design is not correct, can anyone suggest me what should I do? Using SOA? is this correct?

my current solution is run this java project using a bash, but I dont think it is then best idea. I list my class packages

com.company.alteck
com.company.altronics
com.company.gamming
com.company.jaycar
com.company.jup
com.company.rpg
com.company.sansai
com.company.wiretech
com.company.yatsal
com.ebay.api
com.ebay.bean
com.ebay.credential
com.ozsstock.finals
com.ozstock.adapter
com.ozstock.aspectj
com.ozstock.model
com.ozstock.persistence
com.ozstock.service
com.ozstock.suppliers
my structure likes this, all the packages contains "company" should run separately, but depends on the model bean class.

can anyone give me some hints to redesign?