once you have created the pop up menus, you should be able to reposition them, Been a long while since I have used them, as I've found them to be such a hassle to update if the site changes at all.
From memory, you should be able to choose where you want them within the dialoge, and then reposition them manually by selecting the popup (green dotted lines?) and dragging it where you want it to sit.
test with a preview in browser, as I think the browser looks slightly different than the image as a rule.
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Sometimes, when my code just won't behave, I take it outside and make it listen to britney spears music, and when it comes back it's really well behaved. I wonder if it's suffering from post tramatic stress syndrome now..