The magnets do not want to behave. I have 3 pieces of steel temporarily underneath the aluminum magnet holders to attract the magnets while the epoxy sets. I tried just a single piece but that was nearly impossible to remove. These can be moved by sliding them off the end with a hammer and screwdriver after the filler has  set and been finished.
The magnets naturally want to form into a stick. A little bit of filler into about 10 holes and then the magnets can be pushed into the first hole. Then by sliding the next magnet off the top of the first it should just drop into the next hole. And so on. The magnets are always installed with the same pole facing out as required. Polarity needs to be checked before epoxy sets,as the magnets can jump out and turn over faster than you can see.

I use a Hall Effect sensor to check all polarities before the filler sets. This is cheap and easy to make.
The filler used is just common car repair or builders 2 part epoxy filler.