Pop ups are probs best used over boilie. The last thing you want is a pop up hovering over bits n pieces sitting on the deck.
But ultimately the spot itself should dictate when to use a pop up. They're intended to be used when you want the hook/hookbait suspended over a weedy or choddy bottom.
BUT..... I use them for 99.9% of my fishing regardless of the spot or baiting situation. I get proper paranoid about presentation and would rather have a bait that's a little too obvious/blatant than risk the hook point being compromised by a tiny bit of debris/detritus.
If you get them feeding I don't think it matters that much under normal circumstances.