1.) Can you use a modal Window for your pop-up? Users cannot activate an open document window before closing an open dialog (modal) window.
2.) Insert the following into your script that opens the pop-up:
Select Window [ Name: "Your_Pop_Up_Window_Name" ]
If [ Get( WindowName ) ≠ "Your_Pop_Up_Window_Name" ]
New Window [ Name: "Your_Pop_Up_Window_Name" ; …]
Thanks Jade, That answers my second question. Any suggestions on my first question? Some of my windows I would like to close when I leave that window.
Also.. while I have a pro on the line. I have popup windows that I use for quick editing of a record in another window. It's basically a 300px wide data entry window that scrolls. When I'm on that pop up window and I choose to cycle through records, I'd like the main window to cycle through records as well so that the two windows mirror each other. I could use a script like that in a few differet types of situations. Sorry if my explanation is confusing.
Sorry after reviewing I see that your suggestion for my first was to use a "Modal window" I'm not familiar.
Which version of FMP do you have? In v12, you can use the advanced options to specify a "dialog" window for your pop-ups. Users cannot activate an open document window before closing an open dialog window. (Note: this is not the same window style as a custom dialog box.)
i"m not a "pro" by any means so I'll defer your supplemental question to others. You may get a faster reply if you post this in a new thread.
When you define the options in the New Window  scriptstep in v12, you can also specify advanced styles (at the bottom of the dialog box). Click the "Specify" button and choose "Dialog Window (Modal)" style.
IF you are using an older version, there are ways to make a window "modal" with a paused script where closing the window resumes or halts the paused script.