[intellec7]

The way I deal with the Square Hole, round peg issue is I add a point to the center of the square hole (this can be done many ways, I prefer to use the 3 point arc tool and make an arc where the 3 defining points are the midpoints of three edges of the square hole. You can also draw a perpendicular bisector from the one edge to the opposite edge, and the midpoint of the bisector segment is the center of the hole, etc)

Once you have the hole in the center, you need to add an axis. Insert-> Reference Geometry -> Axis. You will select the center point, and the plane/face that the square hole is on. It should automatically draw the axis, but if it doesn't, basically you want to use the axis generation mode where you select a point on the axis and a plane perpendicular to the axis.

So that's how you can get your screw or standoff aligned. Then you can do a Coincidence mate on the face of the plate and the back of the screw/standoff to fix it onto the plate. This constrains the entire piece except for it's rotation in the hole, which really shouldn't be important.