i stack eggs all the time.. its not a big deal at all
you will need to remove any infertile eggs
if , when it comes time for them to hatch, you are still stacking them.. throw out everything you heard about "lockdown" because you will have to open the bator a lot and candle the eggs a lot
as you candle the eggs look for internal pips.. mark those eggs and make sure they are on the top of the pile (I put a mark directly over the internal pip and have that mark facing UP)
as they hatch pull the chicks and the shells and candle the rest again.. marking internal pips and moving them to the top of the pile
The idea is not to have any chicks trying to hatch while on the bottom of the pile.. so yes.. you will be opening the bator a lot until you get the eggs down to one layer
like I said.. it's not a big deal.. and I have gotten 100% hatch rates doing it my way