I never tried to use 2 hard drive magnets. I don't even remember what I did with the other one. To be honest I built this thing last summer and since I didn't have a stir bar, it sat there without ever being fully tested. So I ordered some things from northern brewer and picked up a 25mm stir bar as well. The hard drive magnet kept sending the stir bar to the sides of the apple juice container. I figured either my fan was spinning too fast, the hard drive magnet was to strong, the bottom of the jug was too round, and/or the cigar box lid was too thin. So I had a kind of "why not" moment and saw this magnet stuck to the fridge (I think it had a bottle opener glued to it at one point in time, so it's a little big I suppose) and threw it on the fan and it worked. I didn't glue the magnet down, it sticks to the magnets in the fan motor I'm guessing. (I'm not good with motors, electronics, tools, or anything of that nature.) I don't know if you can tell by the picture but I took a PC fan from an old 486 computer, wired a small power supply that I think came from a charger from a toy RC car, and screwed it to a board, and then stuck the board into an empty box of "It's A Boy" bubble gum cigars.
I have the magnet out towards the outside of the fan blades like in the picture. I tried with the hard drive magnet on the outside and right in the middle and couldn't get either way to work. So funny as it may sound, I just threw this fridge magnet on the middle of the fan and plugged it in. The magnet slides to the outside and the only thing stopping it from being thrown is the fact that the fan blades are just a little lower than the outer "cage" of the fan.
I don't know, I'm not a handy guy and the only money invested into this thing was the $4.25 for the stir bar. Bottom line I guess is that it works so if if you got an old PC sitting around (and you're sick of shaking your yeast starter) you may be able to slop something together like I did. Maybe in the future I'd build myself a nice one but for now this one seems to be working.