The jaw of the vise is normally set so that it is parallel to the x axis. As long as the spindel can cover the opening in the vise it doesn't matter if it is centered. Align the vise's stationary jaw with the spindle. Put a dial indicator on the head and move the table left to right so the indicator rides on the face of the back jaw and keeps the same reading as the table moves. That way when something is clamped in the vise you cut parallel to the edge of the piece. Most of the time you cut as you travel on the on the x axis.
Lets say you want to slot a guard. You start out with a piece of metal an 1" wide and 2" long. Place your parallels in the vise so they hols the piece a bit above the top of the vise jaws with the 2 inch length running the x axis. You can center the cutter by eye or for precision use an edge finder to locate the edge of the material then subtract the radius of the edge finder and move the table on the y axis 1/2 the width of the piece (1/2") plus the radius of the center finder. Measure your y travel with a dial indicator on the front of the table. This will put the cutter in the center of the piece and if the back jaw of the vise is sq with the spindel you will cut straight down the center. You can do the same thing on the x axis if you wish. Then, when you cut you can read how long you are making the slot. Then if you are using a 1/8 cutter to make say a 3/16 slot 3/4 long you can measure the 3/4 on the initial cuts once it is complete and all the way thru you can move the table on the y axis .03 forward and cut it wider. then move the final .00125 and do a finish cut. the move the y axis back .0925 and cut the bask side of the slot wider, then finish with another final of .00125. At least that is how you would do it something like on a precision piece. You can also do the math and make your first cut closer to the front or the back of the slot and then work your way the other direction to get the width you need and keep centered. When you make the first cut to get the rough slot a 1/8 mill will cut over 1/8 wide. The lighter cuts will be more accurate as the cutter deflects less. You can do it all by eye and calibers, but, indicators are easy to keep an eye on and "see" where you actually are