To me it seems natural to write "1.000.000" this way maybe because of the mathematics and such i don't know 
Because of mathematics that's the wrong way to write it....1.000000000000 = 1.
Can't get any simpler than that.
Of course, just use common sense. If someone wants to sell you say 1.000.000 DogeCoins for say 2 bitcoins, it's obvious he's talking about 1 million DogeCoins, not 1 DogeCoin.