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So i have done some magnetizing before but this time im in the process of applying it to 9 tyranid warriors and every single weapon option they have. So i've drilled my holes, but a few of them of course came out a bit uneven, or damaged the upper side of the lip that the magnet sits back in.
So should i glue in the magnets first, or sit the magnet in position, work my green stuff to recreate the lip and then glue? Does it even matter?

Also, as far as keeping track of polarity, of all these so any arm can go to any warrior. My thought was using a larger "master" magnet on my fridge and putting my small magnets on it and painting the face of them black and the back of them white. Anyone have a better faster way?

Thanks for the help guys, i know the questions are kind of base level but they are things i haven't been able to find answers to easily online. And this is by far the biggest project like this i've ever taken on. Man, they have a LOT of options.

On the green stuff question, it depends;

If you think there is enough of a surface in there for the glue to hold, glue the magnet in, then GS over if you think it needs if.

if there is not enough surface, put some gs in it, then put the magnet into the GS. Some people even put a drop of super glue to help the magnet stick to the GS, but that might not be necessary.

Regarding polarization....I make sure all my magnets are polarized the same way. Keep a reference piece/arm/piece of plastic with a magnet on it/whatever in your work area as a sample arm.
Anything that attaches to a body, magnitize it the same as the sample. That way any arm/biomorth/whatever are all magnitized the same.

Then magnetize any body/thing that an arm/biomorth attaches to, the same way.

I've magnetised most of my Tyranid MCs and Tyrant Guard . Yet to do any Warriors or anything smaller but done 2 Tyrants, 2 Tervigons and 2 Trygons, 3 TG.

To add to davethepak's great advice I've found a permanent marker a little better than paint (dries quicker) to mark polarisation. +1 to the use of reference magnets glued onto old bits of sprue.

Also, when the arm joint is smaller or the same size as the magnet or i've broken the "lip", i just lop it off, glue the magnet on and greenstuff the joint over the top of the magnet.

Hope that helps!

Looking forward to magnetising the Haurspex/Exocrine when I get it too! Not sure how the Harpy.Crone will go though....

I manage polarity, I did the following:

1. Took a stick of about 10 1/8" magnets and wrapped them with tape to make a handle and use a pen to mark one end of it.
2. Basically, if you can stick the handle on to any attached magnet, a free magnet on the other end will automatically be oriented correctly for the opposing part. Note whether your pen mark is at the front or the back.
3. As long as your free magnets keep being applied to the proper end, your magnets will always be oriented correctly.

If the hole is too big you could always just drill ab it deeper and pop 2 magnets in if you have enough to spare, I just finished magnetising a whole box of SW termies and all loadouts plus a cyclone launcher I bought separately and I had to use the aforementioned trick on one hole. I love have all these options now.

Thanks for all the great advice guys, its going to help alot. Its really easy to flip those magnets around by accident.