Yes. The head will always be trammed in relation to the table in regards to the y axis. It is actually the column you are adjusting to get your y alignment.

Make sure you start with the column tramming. On the x3 it will also tram the head, but the sx3 has a rotate-able head so the head needs to be adjusted separately. You do this by tightening the two bolts on the side of the head. Make sure when you tram the column you adjust both bolts on either side.

Ill give you an example to make it more clear if its not already. You are facing the mill.
Say the column is leaning to the right a thou and forward a thou. To fix this, I would put a shim under the front right bolt.

Another example is if the column is leaning to the left but is not leaning forward or backward. I would use two shims and put one under each bolt on the left side. You use two because if you only put it under one bolt, it would cause the column to lean a bit back too. But if its under both, it will only adjust the column left and right.