I haven't used prefolds so can't help with most questions... but I did use some eenee pouch pants. Is that what you're referring too? I've never seen eenee pul nappy covers. Do you mean, could you use the prefold instead of the eenee washable pouch inserts? Probably- though I'd imagine they would have to be newborn prefolds as the pouch is pretty small in the pouch pants.
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Thanks Meow yep I meant the pouch pants. I thought I would give this system a go as an inbetween disposables/cloth as DH wants to give them a go too.

Other questions I have...
With prefolds is there any other folding other in folding the two outer lengthwise inwards that needs to be done to put the nappy in the cover? Do you use clasps (not sure what the technical name is) or does it just get shoved in so to speak?

Also I just realised that covers don't have to be PULs. Is that right? You can use fleece/minkee/wool as appropriate covers?

I'm learning so much already!