I would try both situations using good velcro. I covered the hub with velcro and placed velcro on the hd magnets. One magnet worked better for my plate. The velcro holds incredibly well and allows for adjustment. After doing a few starters, I ended up fine-tuning the magnet placement once again. Play around with it. I even figured out you can have the stir bar spinning off-center, creating a bigger vortex and "sweeping" the bottom of the flask (not sure how long the fan would last like that though!)
One is probably going to be the better option. These magnets are polarized end to end, so if you use 2, you'll have 2 North poles and 2 South poles, it'll probably be harder to keep the bar where you want it.