How do I declare my income if all of it comes from paypal ? Most accountants in Portugal (where I live and where this company will be based) don't know how it works... Do I declare it only when I transfer the money to the company's bank account ?
If your accountants don't understand when to declare income, then you have the wrong accountants. I've never met an accountant worth anything that cannot tell you exactly when income must be declared. Try to get a referral to a decent accountant from another businessman there.
Income is income. The source of the income is a minor note in your accounting if you want to keep track of it.
In other words, the source of the money makes no difference. If someone buys your product and sends you $100 from Paypal, or $100 from a credit card, or $100 from a wire transfer, or $100 cash, or $100 from a check- the accounting is the same.