Re: So why do they put those 2 nuts under the thermostat cover?
Oh, Okay..... you're speaking of the two nuts/washers that retain the back portion of the powerhead. I assume you just installed the powerhead to the adapter plate.
Always make sure that the threads on the studs are absolutely clean and not damaged in any way. I always run a die over all threads while I have the component off/apart.
My method on installing those nuts is to have the nut resting on a thin blade, screwdriver tip, whatever, raise it up to meet the stud, then simply spin it on with another thin screwdriver. Works for me every time.