If you have a Live Oak or a Water Oak you will have those problems, Be warned that the Water Oak only lives 50-60 years.
Also if you do build a raised bed try to put a bottom on it to keep the roots out of it- not saying that this will work totally but maybe slow the roots down.
My late father would dig up and chop off some of the roots but they would grow back. Our tree died 2 years ago and I am still digging up roots. I am using the large trunk to grow fines on.
