Is it better to launch the JAVA apps from within the script itself?

I am writing a script that has three apps that I am trying to run tests on.
Internet Explorer
& two java apps that we are building
Case Initiation
Minutes

I have all three applications set to launch in Record and Run Setting. IE launches through the usual browser tab and I have added the direct urls for each of the java applications.
So each line is javaws http://............

The first problem is that multiple instances of the two java applications end up launching. I don't know why. Is it better to launch the JAVA apps from within the script itself?
Second how do I switch between the different applications within the script? I assume I have to make an application active before it will send the steps I recorded for it.

to help more some of the code looks like this:
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' All three apps should get launched Should I have code here that runs each application instead of you the Record Run settings
' Start with Minutes
JavaWindow("Minutes").JavaButton("Execute").Click
JavaWindow("Minutes").JavaDialog("Minutes - Open Session").JavaList("OpenSessionBrowseDialog$DaysCo").Select "23"

' Go to Case Init App
JavaWindow("Case Initiation").JavaEdit("Last:").Set "Hazle"

' Go to Browser
Browser("eCourt - Login").Page("eCourt - Login").WebEdit("username").Set "admin"
--------------------------------------------------------------------

How do I tell QTP to make a particular application active?

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