People can own many companies and it has no bearing on if they have a full time job with someone else. In your case you would setup a 'Limitada' (Ltd) company and this can be done online at https://www.portaldaempresa.pt
I'm from the UK, setting up a company is easy, cheap. Each year I need to submit a small set of accounts, and a tax return. The first time you do this might seem hard, but it's basically form filling, and after the 2nd time it's much easier and simple.
Concentrate on your product, when you take on investment or make profit, look into setting up a company.
I believe it's common for a developer to have their own company to use to sell all their products over their carears.