Add SDS last, just prior to denaturation to avoid preciptation on ice. Use 10-12 uL probe mix per hybridization with regular cover slips, use 20 uL probe mix per hybridization with lifter slips. It's important to cool the probe down before pipetting it onto the array, however you can't place it on ice because the SDS will precipitate. Spin the probe briefly to pellet condensation. Some microfuges which allow the tube to spin through air make a good way of rapidly cooling the tube to Room Temperature.
Place slides in array chambers and align cover slip over arrays.
Check to make sure the slide is right side up. The spots can usually be visualized by breathing on the slide to fog the surface. Little spots of DNA can been seen as the fog evaporates. Pipet probe over the area of the spots and gently place coverslip down, avoiding air bubbles. Fine tip forceps are a great help with this step.