small magnets are a better choice yes, they stay in place a little better however for a charger that's not being moved around you should be fine, just make sure it's not shorting against anything.
The IMR 18650's I have do not have the little button on the Positive side so I use small disc magnets as spacers for them to charge and use in my Provari. They work perfectly.
FWIW most radio shacks stock small rare earth magnets about the size of the button on the positive ends on batteries. They conduct better than common ceramic magnets and are what I use as spacers so I can use 14500's in my e-power.
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