This is all about measuring benefit versus cost. How much will it cost you for supplies in your area, those mainly being acrylic paint and paintbrushes? Some people also use modeling clay and I wouldn't be surprised if other forms of media were used, as well as tools like X-acto knives or what have you. But let's assume you're going bare bones for a while here. While the initial investment of acrylic paint is a loss, it should last for many Amiibos or other artsy **** you feel like doing. Since acrylic is usually easy to get off (moreso when wet), the chance of you damaging your Amiibo isn't that high. (Though, I haven't actually done any customizing myself yet).
So let's say the acrylic paint set and brushes set you back 20 dollars. Assuming the Amiibo was thirteen dollars, you've set back 33 dollars so far, still less than what you would pay for the online customized Amiibo someone else made. If you buy another Amiibo, you'll be set back another 13 dollars, totalling to 46 dollars you've spent. So even if you had to buy two, in reality you're only spending six more dollars. And this isn't considering shipping on the online purchase, nor is it considering the fact you already might have supplies like you said.
Tl;dr, try to do it yourself first! It's always fun to try stuff like that, and you eventually get better at it and have the pride that you made that customization. Plus you most likely break even in the long run.
