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It seems you are better off moving large amounts rather than lots of smaller ones but i could be wrong

Well if you're just trading as long as the fees are a % of the trade it doesn't matter.

But withdrawal fees are usually fixed and for example Kraken will charge you about 1.7$ to withdraw ethereum, if you only want to withdraw 10$ you'll end up with 8.2$, that's a big difference.

If you wait and withdraw 1000$ then the fee becomes nothing in comparison.