You really will need to start by talking to an accountant in Portugal, and run through how your freelance work works. If you set things up the wrong way, you may well end up paying too much tax (by being unable to offset enough of your expenses, for example). Advice not based on a full understanding of your situation is likely to be well-intentioned by inaccurate.
If you want to be able to visit your accountant on any frequency, it will help the forum to know where you are/will be based. I have used a good Algarve-based accountant in the past; my current one is not currently recommendable, sadly, though very pleasant.
Having had experience of various banks, we have moved both personal and business banking to Crédito Agrícola. They are a mutual, rather than a profit-driven, bank, and claim to have a particular interest in supporting small businesses. We have been delighted by the ease of service.
However, service can vary from branch to branch within the same bank brand. With Novo Banco (before this) we had a wonderful advisor in Queluz; but here in Santarém, their disinterest and borderline rudeness was palpable.
Whoever you go with, check all charges. Some lead with "no charge for X", but actually charge for something different, that another one doesn't, making it hard to draw full comparisons at a glance. There are online banks (many of which are owned by major banks, like Moey! from Crédito Agrícola) - these often have lower headline charges, but not always the full range of services for business banking, etc.
Some banks (notably Santander and BPI, to my knowledge) are in the process of reducing their branch network, so if in-person access is important, this may be worth asking about.