I typically mount a test indicator ( I use a tenths indicator, one could use 50 millionths ) in the spindle.
Then tram the table in X & Y. Use the tramming to detect imperfections in the bed/table and adjust out by whatever means you can depending on the type of machine configuration you have.
Once this is complete, Then mount the same indicator in some type of holder ( I use a magnetic base or one of several I made ) that will enable you to rotate the indicator on an arc. To be clear, the indicator will not be aligned with the spindle in Z axis, rather offset 3", 4" , 8" ( the more the more accurate ). Rotate the spindle and take readings ( example readings X+,X-,Y+,Y-. Now adjust the head to bring all readings to zero.
Once you get this close, but perhaps are still uncertian or several tenths or thousandths off...skim cut the table if you want it as close as you can get it. Most machine manufacturers ( both routers and mills ) machine their tables with the spindle on the machine.
Hope this helps!