You deal with them by using the tax rules that are set out, and buy getting an accountant to make sure you are adhering to them.
Any issues that arise about revenue if you have to start charging vat are due to your pricing, not the Vat rules.
If you do business within EU with other countries you have to register for VAT and charge it. Then you have to get customer info and charge what his country charges....it's a mess.
You're correct though, I misunderstood your question, it seems you're not even at that stage yet. You should really talk to an accountant, not HN. They will tell you exactly what you need to be doing.
Doing Vattable business with other EU countries is a pain. You will need whether each customer is vat registered in their particular country and either charge Vat or not based upon that.
Are you doing business to business sales, or business to customer?