You put the trim in the saw in the same orientation that it will be installed. If you're dealing with a square corner with intersecting 1/4 round, then a standard 45* cut will do the job, adjusting the cut angle slightly for any variance in the corner angle.
If you're transitioning a vertical molding into a horizontal molding, then the cut is only minorly different, in that you'll have to figure out how to position the trim in the saw to get the miter in the correct orientation. It will help if you set the molding into the corner and mark the face with a pencil to indicate the angle of the cut and positioning in the saw. The pencil mark is merely for reference, it is not a cut line or angle marking.
Example: Set the molding on the floor and but it into the corner. Set your pencil at the top edge where it meets the corner and draw a line away from the corner down the face to the bottom edge of the trim. Again, this is only a reference line to show you how it needs to sit in the saw and the direction of the miter, it does not need to be drawn completely from top to bottom on the face of the trim.