I agree with
@davidpbest that it is important that the spindle axis be parallel to the column on a square column mill. In addition, the quill, if equipped, (my Tormach CNC has only the column for z axis motion) has to be parallel to the spindle axis.
If a square is used, it must be a precision square. Verification of squareness is rather difficult without a precision square to use as a reference. Rather, I used a modification of the RDM method to determine parallelness of the spindle axis to the column. It should be done in both x and y direction. Mount a rigid bar known to be good regarding diameter and roundness in the spindle. I used an R8 collet for this purpose. Mount a test indicator so it contacts the bar near the collet when the quill is extended. rotate the spindle and note the minimum and maximum readings. Average the readings. Retract the spindle and repeat the rotation and readings. If the spindle is parallel to the quill, the averages will be the same. Do this in both x and y directions. It is unlikely that there will be a means for correcting any out of parallel situation but it is good to know if a it exists.
Repeat this process with the quill fixed in a retracted position, this time moving the column to determine parallelness between the spindle and the column. Correct any out of parallel situation by rotating or shimming the head. Once the spindle is parallel to the column, the usual procedure for tramming the head can be used but rather than rotating the head, the column would be shimmed to correct any non perpendicular situation between the spindle and the x and y ways.
One thing to note. The primary reason that tramming is done is to make sure the spindle axis is perpendicular to the ways so that successive passes don't result in cutting steps and the front and rear of the cutter contacts the surface equally. This test is really referencing the ways and if the table isn't parallel with the ways, using the top of the table as the surface trammed will result in an inaccurate tram. This also hold true if tramming to a vise or any other surface on the table. To work around this, before tramming, I mount a sacrificial surface to the table and skim the surface with a 1/4" end mill. the small diameter end mill will minimize any effect caused by an out of tram condition. This surface will be parallel to the x and y ways. Then tram using that surface in the usual fashion.
On another note, on a mill with a square collumn, the z axis gibs should be adjusted for minimum free play consistent with free movement. Excessive play will result in nod of the head due to its cantilevered weight. When making these tests, lock the quill and column before making measurements (not something I can do with my CNC mill, unfortunately).