Visa Question (UK)

I’ve been in Taiwan for a month or so looking for work and have started worrying about visa issues when I eventually get my working visa. My concern is that I don’t have a paper visa as I was told that if I have a return flight within 90 days (which I do) then I am allowed to stay in Taiwan for the 90 days without a problem. Will the lack of paper visa cause problems when it comes time for me to get my working visa?