We often used 2 pf at night and a cover, no problem. Or a doubler. It looks funny but baby seems fine. I stopped changing at night when he stopped pooping at night.
Okay- these things are all sort of obvious, perhaps, but I made these mistakes... the cover has to really fit well for no leaks. If its too small or anything- won't work right. Make sure the diaper is really totally inside the cover- anything hanging out even the least little bit will wick moisture out. Also, some PJs sort of dig in at the waist or something and will wick moisture out.
My son has had way more nighttime leaking with disposable diapers than with cloth. I am not sure why, but there you go.
When my son was a lot older I discovered the joys of a wool soaker (he grew out of all the covers we had so I was looking around). They are amazing, they really have worked well for us. You just have to keep them lanolized. It its just for nighttime, you can get away with just one (once in a while when its washing/drying you might need to use a regular cover- they can take a long time to dry. But we only washed/lanolized once a month since it was just for nighttime). I even ended up making one out of an old sweater for a grand total of $1 and about an hour of my own labor (which, sadly, is pretty cheap these days).