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This is my first time building terrain from GW and was wondering if anyone used magnets at all with theirs. I am looking at the pieces and there are many different layouts that are possible and thought magnets could help change it up for different missions. The pieces are the alchomite stacks.

Could you post a picture or a link to the terrain piece?

With the “normal” ruined buildings, magnetizing the levels is a great idea. In smaller games, single or double story ruins are great, and it’s good to have several. With bigger games, you have the option to stack taller structures, to block LOS to large models, like Knights.

Yup, you're a genius. Go for it.
Although, with terrain pieces being quite large there is quite often the option to make a mechanical fixing such as holes and pegs, rails, nuts and bolts, tube extensions/collars etc that could well provide more flexibility and stability than magnets.
You'll soon find that polarity can cause issues with a magnet set up whereas good old fashioned holes and pegs will work way better even though it initially seems a bit low tech.
Additionally, magnets can get expensive fast, especially if you need honking big ones for larger sub assemblies. Price it out by all means but you might find that it's not too much of a stretch to buy another kit and build that in the alternate configuration.

I put magnets on old Citadel Wood tree bases. They were just too strong and did their job too well

I also tried magnetizing Sector Mechanicus pipes, chimneys, etc. The end result was too wobbly. I wouldn't try to magnetize other buildings, seems like too much trouble for something that might not even work properly.

I didn't think to add a link or picture. Here is the link to it in the GW site.

https://www.games-workshop.com/en-US/Sector-Mechanicum-Alchomite-Stack?_requestid=2474575

I hadn't thought of using a hole and peg system may need to look into something like that.

Well, the only reason to leave that in pieces would be for storage. In terms of play, I don’t think that would break down into smaller pieces.

But yes, peg-and-hole can also work just fine.

You should checkout archon studios. They did a set of terrain that's a great value. They already have holes for magnets. They come with pegs or you can buy magnets instead.

They just came out with 2 new designs. One looks mechanicus-ish.