When launching apps by AppleScript, how do you keep them in the background, & not take focus away from other apps that may be running at the same time?
That depends on how you launch them.
AppleScript has two direct commands to launch an application in addition to indirect commands which will open an app if it's not already running):
activate -- bring an application frontmost and launch it if it's not already running
launch -- open the application in the background
So you should try using 'launch' instead of 'activate'.
The windows will still be visible, but it will launch behind the frontmost app so you don't lose focus. Note though that some commands (especially System Events and UI scripting commands) require the application to be frontmost so you should look at what you're trying to do once it's open to see if it truly is viable to run in the background.